fix(tools): name the committed files when a patch is partially applied

Review follow-up for #956. When a later change in a multi-file patch fails
(for example the pre-commit recheck refuses a file that changed after
planning), the error now lists exactly which files were already committed
and states that the rest are unchanged, instead of a generic "partially
applied" warning. The model can then re-read only what actually changed.

Test: a three-file structured patch whose second file is altered after
planning fails with "already committed: first.txt", first.txt holds the
patched content, and the other two files are untouched.

Co-Authored-By: Claude Fable 5 <[email protected]>
Claude-Session: https://claude.ai/code/session_012JqvAf7zsP1qYFVZayKXHq

internal/agent/prompt_budget_test.go

@@ -68,7 +68,7 @@ func TestEagerToolSchemaTokenBudget(t *testing.T) {
 	}
 }
 
-func TestAgentAdvertisesPatchInsteadOfAmbiguousStringReplacement(t *testing.T) {
+func TestAgentAdvertisesBothEditTools(t *testing.T) {
 	registry := tools.NewRegistry()
 	for _, tool := range tools.CoreToolsScoped(t.TempDir(), nil) {
 		registry.Register(tool)
@@ -79,9 +79,9 @@ func TestAgentAdvertisesPatchInsteadOfAmbiguousStringReplacement(t *testing.T) {
 		names[definition.Name] = true
 	}
 	if !names["apply_patch"] {
-		t.Fatal("agent must retain apply_patch for existing-file changes")
+		t.Fatal("agent must retain apply_patch for multi-hunk changes")
 	}
-	if names["edit_file"] {
-		t.Fatal("agent must not receive the ambiguous string-replacement tool")
+	if !names["edit_file"] {
+		t.Fatal("agent must receive edit_file for targeted exact replacements")
 	}
 }

internal/agent/system_prompt.md

@@ -52,7 +52,7 @@ work.
 
 - Choose the narrowest tool that safely accomplishes the step. Prefer native
   file tools - read_file, read_minified_file, list_directory, glob, grep,
-  write_file, apply_patch - over shelling out to
+  edit_file, apply_patch, write_file - over shelling out to
   cat/sed/awk/python for file operations.
   They are safer, reviewable, and produce clean diffs.
 - Prefer read_minified_file when initially exploring source code; it preserves
@@ -61,11 +61,18 @@ work.
 - Keep edits focused and reviewable. A single patch may update several related
   files when they form one coherent change; do not hide unrelated edits in a
   bulk shell or script rewrite.
-- For edits to existing files, prefer apply_patch with minimal, targeted hunks
-  and enough unchanged context to identify the intended location. Match the
-  existing indentation, imports, and idioms. Match the file's comment density:
-  do not add explanatory comments unless the user asks or the code is already
+- For edits to existing files, use edit_file for a targeted change (old_string
+  must match the file exactly and be unique, so include a few surrounding
+  lines) and apply_patch when one coherent change spans several hunks or
+  files. Use write_file only to create a file or when most of it changes; do
+  not rewrite a whole file to change a few lines. Match the existing
+  indentation, imports, and idioms. Match the file's comment density: do not
+  add explanatory comments unless the user asks or the code is already
   comment-dense.
+- A successful edit result already confirms the change; do not re-read a file
+  just to verify an edit that succeeded. If an edit fails, read the error, fix
+  the old_string or hunk, and retry the same tool rather than switching to a
+  full rewrite.
 - Solve the problem as posed, not a more general version of it. Add no
   speculative abstraction, configurability, or handling for cases that cannot
   occur, and nothing the user did not ask for. A small diff can still be
@@ -105,7 +112,7 @@ work.
   you need to clean up a running foreground command yourself, use write_stdin.
 - write_stdin's session_id is only ever an id returned by a still-running
   exec_command; never guess or probe ids. If you have no such session, start one
-  with exec_command, or use write_file/apply_patch for file changes.
+  with exec_command, or use edit_file/apply_patch/write_file for file changes.
 - write_stdin with empty input polls an existing exec_command session, and
   `\u0003` interrupts it. Sending other stdin bytes may require approval because
   it can drive the running process beyond the original command. Non-tty sessions

internal/agent/system_prompt_models.go

@@ -60,14 +60,18 @@ const openAIPromptAddendum = `<model_guidance>
   longer answers, fenced code blocks for code, and ` + "`inline code`" + ` for paths,
   commands, and symbols.
 - Strongly prefer the native file tools (read_file, list_directory, grep, glob,
-  write_file, apply_patch) over shelling out to cat/sed/awk/python for
-  file work. Make one tool call per file; do not batch file writes into a script.
+  edit_file, apply_patch, write_file) over shelling out to cat/sed/awk/python
+  for file work. read_file, edit_file and write_file take one file per call;
+  a single apply_patch may span several files when they form one coherent
+  change. Do not batch file writes into a script. Independent tool calls
+  (several reads, several edit_file calls to different files) belong in the
+  same turn.
 - Persist until the task is fully handled this turn: gather context, implement,
   run the validators, and report — do not stop at a partial result.
 </model_guidance>`
 
 const geminiPromptAddendum = `<model_guidance>
-- Prefer the dedicated tools (read_file, grep, glob, apply_patch) over
+- Prefer the dedicated tools (read_file, grep, glob, edit_file, apply_patch) over
   equivalent shell commands; they are safer and produce cleaner diffs.
 - Be concise and concrete. When you run a shell command with side effects, state
   in one short clause why it is needed.

internal/agent/system_prompt_test.go

@@ -36,7 +36,7 @@ func TestCoreSystemPromptIncludesCodingQualityRules(t *testing.T) {
 		"inspect the target file",
 		"plan then act",
 		"choose the narrowest tool",
-		"for edits to existing files, prefer apply_patch",
+		"for edits to existing files, use edit_file",
 		"verify after edits",
 		"honor the active permission mode",
 		"avoid broad refactors",

internal/sandbox/apply_patch_paths_test.go

@@ -0,0 +1,96 @@
+package sandbox
+
+import (
+	"path/filepath"
+	"strings"
+	"testing"
+)
+
+func TestApplyPatchPathBlockOnlyRejectsRelativeTraversal(t *testing.T) {
+	root := t.TempDir()
+	inside := filepath.Join(root, "main.js")
+	structured := func(path string) string {
+		return strings.Join([]string{"*** Begin Patch", "*** Update File: " + path, "@@", "-a", "+b", "*** End Patch"}, "\n")
+	}
+	for name, patch := range map[string]string{
+		"absolute inside workspace": structured(inside),
+		"relative":                  structured("main.js"),
+		"decorated markers":         "*** Begin Patch ***\n*** Update File: main.js\n@@\n-a\n+b\n*** End Patch ***",
+		"no-space marker":           "***Begin Patch\n*** Update File: main.js\n@@\n-a\n+b\n***End Patch",
+	} {
+		request := Request{ToolName: "apply_patch", WorkspaceRoot: root, SideEffect: SideEffectWrite, Args: map[string]any{"patch": patch}}
+		if block := applyPatchPathBlock(request); block != nil {
+			t.Fatalf("%s: unexpected block %+v", name, block)
+		}
+	}
+	for _, path := range []string{"../escape.js", ".."} {
+		for name, patch := range map[string]string{"canonical": structured(path), "no-space": "***Begin Patch\n*** Update File: " + path + "\n@@\n-a\n+b\n***End Patch"} {
+			request := Request{ToolName: "apply_patch", WorkspaceRoot: root, SideEffect: SideEffectWrite, Args: map[string]any{"patch": patch}}
+			block := applyPatchPathBlock(request)
+			if block == nil || block.Code != BlockOutsideWorkspace {
+				t.Fatalf("%s %q must be blocked as traversal, got %+v", name, path, block)
+			}
+		}
+	}
+}
+
+// Every marker spelling the tool applies must be classified as structured at
+// the sandbox boundary too; otherwise the boundary scans the patch as a unified
+// diff, extracts no targets, and validates nothing (fail-open).
+func TestStructuredPatchClassifierMatchesToolSpellings(t *testing.T) {
+	for _, header := range []string{"*** Begin Patch", "*** Begin Patch ***", "***Begin Patch", "  *** Begin Patch  ", "\ufeff*** Begin Patch"} {
+		patch := header + "\n*** Update File: main.js\n@@\n-a\n+b\n*** End Patch"
+		if !IsStructuredPatch(patch) {
+			t.Fatalf("%q must classify as a structured patch", header)
+		}
+		if paths := applyPatchPaths(patch); len(paths) != 1 || paths[0] != "main.js" {
+			t.Fatalf("%q: sandbox must extract the structured target, got %v", header, paths)
+		}
+	}
+	for _, header := range []string{"--- a/x", "Begin Patch", "*** Begin Patchwork", "*** Update File: x"} {
+		if IsStructuredPatch(header + "\n-a\n+b") {
+			t.Fatalf("%q must not classify as a structured patch", header)
+		}
+	}
+	if StructuredPatchMarker("*** End Patch ***") != "end" || StructuredPatchMarker("***End Patch") != "end" {
+		t.Fatal("decorated end markers must classify as end")
+	}
+}
+
+func TestApplyPatchRequestPathsCarryAbsolutePathsToScopeValidation(t *testing.T) {
+	root := t.TempDir()
+	// NewScope also grants the system temp dir, so a sibling t.TempDir() is
+	// legitimately in scope; pick a path under the filesystem root instead.
+	outside, err := filepath.Abs(filepath.Join(string(filepath.Separator), "zero-outside-workspace-test", "escape.js"))
+	if err != nil {
+		t.Fatal(err)
+	}
+	scope, err := NewScope(root, nil)
+	if err != nil {
+		t.Fatal(err)
+	}
+	inside := filepath.Join(root, "main.js")
+	structured := func(header, footer, path string) string {
+		return strings.Join([]string{header, "*** Update File: " + path, "@@", "-a", "+b", footer}, "\n")
+	}
+	for name, spelling := range map[string][2]string{"canonical": {"*** Begin Patch", "*** End Patch"}, "no-space": {"***Begin Patch", "***End Patch"}} {
+		// Failure path: the exact path the boundary parsed must be denied by the
+		// scope. structuredPatchHeaderPaths normalises separators to "/", so the
+		// parsed form is compared in slash form and then validated as-is.
+		paths := applyPatchRequestPaths(map[string]any{"patch": structured(spelling[0], spelling[1], outside)})
+		if len(paths) != 1 || paths[0] != filepath.ToSlash(outside) {
+			t.Fatalf("%s: absolute patch path must reach scope validation unchanged, got %v", name, paths)
+		}
+		if block := scope.validate(paths[0]); block == nil || block.Code != BlockOutsideWorkspace {
+			t.Fatalf("%s: scope must deny the parsed outside path %q, got %+v", name, paths[0], block)
+		}
+		// Success path: the parsed inside path must be accepted by the scope.
+		paths = applyPatchRequestPaths(map[string]any{"patch": structured(spelling[0], spelling[1], inside)})
+		if len(paths) != 1 || paths[0] != filepath.ToSlash(inside) {
+			t.Fatalf("%s: inside patch path must reach scope validation unchanged, got %v", name, paths)
+		}
+		if block := scope.validate(paths[0]); block != nil {
+			t.Fatalf("%s: scope must accept the parsed inside path %q, got %+v", name, paths[0], block)
+		}
+	}
+}

internal/sandbox/risk.go

@@ -281,11 +281,15 @@ func applyPatchPathBlock(request Request) *pathBlock {
 	if patch == "" {
 		return nil
 	}
+	// Only relative traversal is rejected up front. Absolute paths flow through
+	// the regular workspace-scope validation below (requestPaths), which accepts
+	// one inside the workspace and denies one outside — a model that echoes the
+	// absolute path read_file showed it must not be blocked for that alone.
 	for _, path := range applyPatchPaths(patch) {
 		if path == "" || path == "/dev/null" {
 			continue
 		}
-		if filepath.IsAbs(path) || path == ".." || strings.HasPrefix(path, "../") {
+		if path == ".." || strings.HasPrefix(path, "../") {
 			return &pathBlock{
 				Code:   BlockOutsideWorkspace,
 				Path:   path,
@@ -296,8 +300,35 @@ func applyPatchPathBlock(request Request) *pathBlock {
 	return nil
 }
 
+// structuredPatchMarkerPattern is the single classifier for structured-patch
+// markers, shared by the sandbox boundary and the apply_patch tool (which
+// imports this package). It accepts the canonical "*** Begin Patch" /
+// "*** End Patch" and the decorated spellings models emit ("*** Begin Patch ***",
+// "***Begin Patch", trailing whitespace). Both sides must agree: a spelling the
+// tool would apply but the sandbox did not recognise would make the sandbox
+// scan the patch as a unified diff, extract no targets, and validate nothing.
+var structuredPatchMarkerPattern = regexp.MustCompile(`^\*{3}\s*(Begin|End) Patch\s*\**\s*$`)
+
+// StructuredPatchMarker classifies a line as the "begin" or "end" marker of a
+// structured patch, or "" when it is neither.
+func StructuredPatchMarker(line string) string {
+	match := structuredPatchMarkerPattern.FindStringSubmatch(strings.TrimSpace(line))
+	if match == nil {
+		return ""
+	}
+	return strings.ToLower(match[1])
+}
+
+// IsStructuredPatch reports whether patch opens with a structured begin marker.
+// The tool applies exactly the patches this returns true for, so the sandbox
+// extracts structured header paths for exactly the same set.
+func IsStructuredPatch(patch string) bool {
+	first, _, _ := strings.Cut(strings.TrimSpace(strings.TrimPrefix(patch, "\ufeff")), "\n")
+	return StructuredPatchMarker(first) == "begin"
+}
+
 func applyPatchPaths(patch string) []string {
-	if strings.HasPrefix(strings.TrimSpace(strings.TrimPrefix(patch, "\ufeff")), "*** Begin Patch") {
+	if IsStructuredPatch(patch) {
 		return structuredPatchHeaderPaths(patch)
 	}
 	return patchHeaderPaths(patch)

internal/tools/apply_patch.go

@@ -3,11 +3,11 @@ package tools
 import (
 	"context"
 	"fmt"
-	"os"
-	"os/exec"
 	"path/filepath"
 	"strconv"
 	"strings"
+
+	"github.com/Gitlawb/zero/internal/sandbox"
 )
 
 type applyPatchTool struct {
@@ -20,11 +20,11 @@ func NewScopedApplyPatchTool(workspaceRoot string, scope PathScope) Tool {
 	return applyPatchTool{
 		baseTool: baseTool{
 			name:        "apply_patch",
-			description: "Apply a patch inside the workspace or an explicitly granted extra write root.",
+			description: "Apply a multi-hunk or multi-file patch inside the workspace (or a granted extra write root). Structured format:\n*** Begin Patch\n*** Update File: src/app.js\n@@\n unchanged context line\n-removed line\n+added line\n*** End Patch\nUse \"*** Add File: path\" with \"+\" lines to create a file and \"*** Delete File: path\" to remove one; several sections may follow each other. A unified diff (---/+++ headers with a/ b/ prefixes, @@ hunks) is also accepted and applied in-process. Paths are workspace-relative; absolute paths inside the workspace are fine. For a single targeted change, edit_file is simpler.",
 			parameters: Schema{
 				Type: "object",
 				Properties: map[string]PropertySchema{
-					"patch": {Type: "string", Description: "A unified diff or a structured *** Begin Patch patch to apply."},
+					"patch": {Type: "string", Description: "The structured (*** Begin Patch) or unified-diff patch text."},
 					"cwd":   {Type: "string", Description: "Directory where the patch should be applied. Relative paths stay in the workspace; use an absolute path to target a granted extra write root. Defaults to workspace root.", Default: "."},
 				},
 				Required:             []string{"patch"},
@@ -59,177 +59,14 @@ func (tool applyPatchTool) RunWithOptions(ctx context.Context, args map[string]a
 	if isStructuredPatch(patch) {
 		return tool.runStructuredPatch(applyRoot, relativeRoot, patch, options)
 	}
-	if err := validatePatchPaths(applyRoot, patch); err != nil {
-		return errorResult("Error applying patch: " + err.Error())
-	}
-
-	tempFile, err := os.CreateTemp("", "zero-patch-*.patch")
+	// Unified diffs are translated into the same operations and applied by
+	// the same os.Root engine, so neither format opens a target by pathname
+	// after validation (no check-to-use window) and git is not needed.
+	operations, err := parseUnifiedPatch(patch)
 	if err != nil {
 		return errorResult("Error applying patch: " + err.Error())
 	}
-	patchPath := tempFile.Name()
-	defer func() {
-		_ = os.Remove(patchPath)
-	}()
-	if _, err := tempFile.WriteString(patch); err != nil {
-		_ = tempFile.Close()
-		return errorResult("Error applying patch: " + err.Error())
-	}
-	if err := tempFile.Close(); err != nil {
-		return errorResult("Error applying patch: " + err.Error())
-	}
-
-	if err := recheckPatchWriteTargets(applyRoot, patch); err != nil {
-		return errorResult("Error applying patch: " + err.Error())
-	}
-	var createdTargets []string
-	var fullySuppliedTargets []string
-	wholeBefore := map[string]bool{}
-	if options.FileTracker != nil {
-		createdTargets = missingPatchTargets(applyRoot, patch)
-		fullySuppliedTargets = completeCreatedPatchTargets(applyRoot, patch)
-		for _, path := range patchHeaderPaths(patch) {
-			if path == "" || path == "/dev/null" {
-				continue
-			}
-			if absolute, _, rerr := resolveWorkspaceTargetPath(applyRoot, path); rerr == nil {
-				wholeBefore[absolute] = options.FileTracker.SeenWhole(absolute)
-			}
-		}
-	}
-
-	command := exec.CommandContext(ctx, "git", "apply", "--whitespace=nowarn", patchPath)
-	command.Dir = applyRoot
-	output, err := command.CombinedOutput()
-	if err != nil {
-		message := strings.TrimSpace(string(output))
-		if message == "" {
-			message = err.Error()
-		}
-		return errorResult("Error applying patch: " + message)
-	}
-
-	summary := "Patch applied successfully."
-	if relativeRoot != "." {
-		summary = "Patch applied successfully in " + relativeRoot + "."
-	}
-	result := okResult(summary)
-	result.ChangedFiles = changedFilesFromPatch(relativeRoot, patch)
-	result.Display = Display{Summary: summary, Kind: "diff", Preview: capPreviewDiff(patch)}
-	fullySupplied := make(map[string]bool, len(fullySuppliedTargets))
-	for _, absolute := range fullySuppliedTargets {
-		fullySupplied[absolute] = true
-	}
-	// Re-baseline files changed by this tool. When the model had already seen the
-	// whole input (or supplied a complete new file), the exact patch plus that
-	// input determines the whole output, so a follow-up edit needs no wasted read.
-	// Partial observations remain conservative and are cleared by Record.
-	for _, changed := range result.ChangedFiles {
-		if absolute, _, rerr := resolveScopedPath(tool.workspaceRoot, tool.scope, changed); rerr == nil {
-			content, readErr := os.ReadFile(absolute)
-			if readErr != nil {
-				options.FileTracker.Forget(absolute)
-				continue
-			}
-			info, _ := os.Stat(absolute)
-			wasWhole := wholeBefore[absolute] || fullySupplied[absolute]
-			options.FileTracker.Record(absolute, content, info)
-			if wasWhole {
-				lines := lineCount(string(content))
-				options.FileTracker.RecordSeenRange(absolute, 1, lines, lines)
-			}
-		}
-	}
-	recordCreatedPatchTargets(options.FileTracker, createdTargets)
-	return result
-}
-
-func missingPatchTargets(root string, patch string) []string {
-	seen := map[string]bool{}
-	var missing []string
-	for _, path := range patchHeaderPaths(patch) {
-		if path == "" || path == "/dev/null" {
-			continue
-		}
-		absolute, _, err := resolveWorkspaceTargetPath(root, path)
-		if err != nil || seen[absolute] {
-			continue
-		}
-		seen[absolute] = true
-		if _, err := os.Stat(absolute); os.IsNotExist(err) {
-			missing = append(missing, absolute)
-		}
-	}
-	return missing
-}
-
-// completeCreatedPatchTargets returns only files whose full contents are
-// supplied by a /dev/null creation patch. A missing rename/copy destination is
-// created by git too, but its bytes come from an unread source and must not gain
-// whole-file observation credit.
-func completeCreatedPatchTargets(root string, patch string) []string {
-	seen := map[string]bool{}
-	var created []string
-	oldRemaining, newRemaining := 0, 0
-	inHunk := false
-	fromDevNull := false
-	for _, line := range strings.Split(strings.ReplaceAll(patch, "\r\n", "\n"), "\n") {
-		if inHunk && (oldRemaining > 0 || newRemaining > 0) {
-			switch {
-			case strings.HasPrefix(line, "-"):
-				oldRemaining--
-			case strings.HasPrefix(line, "+"):
-				newRemaining--
-			case strings.HasPrefix(line, "\\"):
-			default:
-				oldRemaining--
-				newRemaining--
-			}
-			continue
-		}
-		inHunk = false
-		switch {
-		case strings.HasPrefix(line, "diff --git "):
-			fromDevNull = false
-		case strings.HasPrefix(line, "@@"):
-			oldRemaining, newRemaining = parseHunkCounts(line)
-			inHunk = oldRemaining > 0 || newRemaining > 0
-		case strings.HasPrefix(line, "--- "):
-			fromDevNull = patchFileHeaderPath(line) == "/dev/null"
-		case strings.HasPrefix(line, "+++ "):
-			path := patchFileHeaderPath(line)
-			if !fromDevNull || path == "" || path == "/dev/null" {
-				fromDevNull = false
-				continue
-			}
-			fromDevNull = false
-			absolute, _, err := resolveWorkspaceTargetPath(root, stripPatchPrefix(path))
-			if err != nil || seen[absolute] {
-				continue
-			}
-			if _, err := os.Stat(absolute); !os.IsNotExist(err) {
-				continue
-			}
-			seen[absolute] = true
-			created = append(created, absolute)
-		}
-	}
-	return created
-}
-
-func recordCreatedPatchTargets(tracker *FileTracker, missingBefore []string) {
-	if tracker == nil {
-		return
-	}
-	for _, absolute := range missingBefore {
-		if _, err := os.Stat(absolute); err != nil {
-			continue
-		}
-		if resolved, err := filepath.EvalSymlinks(absolute); err == nil {
-			absolute = resolved
-		}
-		tracker.RecordCreated(absolute)
-	}
+	return applyPatchOperations(applyRoot, relativeRoot, operations, options)
 }
 
 // changedFilesFromPatch extracts the unique, WORKSPACE-relative paths a patch
@@ -260,27 +97,35 @@ func changedFilesFromPatch(relativeRoot string, patch string) []string {
 	return paths
 }
 
+// normalizePatchPathForRoot resolves platform-level symlinks (macOS /var ->
+// /private/var) in the prefix of an absolute patch path that lies outside the
+// apply root, so a path the model copied from read_file compares equal to the
+// symlink-resolved root. Relative paths are returned unchanged.
+func normalizePatchPathForRoot(root string, path string) string {
+	if !filepath.IsAbs(path) {
+		return path
+	}
+	resolvedRoot, err := filepath.Abs(root)
+	if err != nil {
+		return path
+	}
+	if evaluated, err := filepath.EvalSymlinks(resolvedRoot); err == nil {
+		resolvedRoot = evaluated
+	}
+	return sandbox.NormalizePrefixForRoot(path, resolvedRoot)
+}
+
 func validatePatchPaths(root string, patch string) error {
 	for _, path := range patchHeaderPaths(patch) {
 		if path == "" || path == "/dev/null" {
 			continue
 		}
-		if filepath.IsAbs(path) || path == ".." || strings.HasPrefix(path, "../") {
+		// Relative traversal is rejected here; an absolute path is checked by
+		// resolveWorkspaceTargetPath, which only accepts one inside the root.
+		if path == ".." || strings.HasPrefix(path, "../") {
 			return fmt.Errorf("patch path %q must stay inside the workspace", path)
 		}
-		if _, _, err := resolveWorkspaceTargetPath(root, path); err != nil {
-			return err
-		}
-	}
-	return nil
-}
-
-func recheckPatchWriteTargets(root string, patch string) error {
-	for _, path := range patchHeaderPaths(patch) {
-		if path == "" || path == "/dev/null" {
-			continue
-		}
-		if err := recheckWorkspaceWriteTarget(root, path); err != nil {
+		if _, _, err := resolveWorkspaceTargetPath(root, normalizePatchPathForRoot(root, path)); err != nil {
 			return err
 		}
 	}
@@ -351,7 +196,7 @@ func patchFileHeaderPath(line string) string {
 // tokens. Scanning the whole line would let a crafted heading like
 // "@@ -1,1 +1,1 @@ +1,999999" overwrite the real count, keep the parser stuck in
 // hunk mode, and swallow later "--- "/"+++ " file headers so they escape
-// validatePatchPaths / recheckPatchWriteTargets — a workspace-confinement bypass.
+// validatePatchPaths — a workspace-confinement bypass.
 func parseHunkCounts(line string) (int, int) {
 	_, rest, ok := strings.Cut(line, "@@")
 	if !ok {

internal/tools/apply_patch_tolerance_test.go

@@ -0,0 +1,712 @@
+package tools
+
+import (
+	"context"
+	"os"
+	"path/filepath"
+	"strconv"
+	"strings"
+	"testing"
+)
+
+// Models routinely decorate the structured markers ("*** Begin Patch ***") and
+// write unified-diff ranges after "@@"; both used to fail on the first line and
+// pushed the model into whole-file rewrites.
+func TestApplyPatchToleratesDecoratedMarkersAndRangeHeaders(t *testing.T) {
+	root := t.TempDir()
+	writeTestFile(t, filepath.Join(root, "hello.txt"), "hello\nold\nbye\n")
+
+	patch := strings.Join([]string{
+		"*** Begin Patch ***",
+		"*** Update File: hello.txt",
+		"@@ -1,3 +1,3 @@",
+		" hello",
+		"-old",
+		"+new",
+		"*** End Patch ***",
+		"",
+	}, "\n")
+
+	if !isStructuredPatch(patch) {
+		t.Fatal("decorated begin marker must still be recognised as a structured patch")
+	}
+	result := NewScopedApplyPatchTool(root, nil).Run(context.Background(), map[string]any{"patch": patch})
+	if result.Status != StatusOK {
+		t.Fatalf("decorated structured patch should apply, got %s: %s", result.Status, result.Output)
+	}
+	content, err := os.ReadFile(filepath.Join(root, "hello.txt"))
+	if err != nil {
+		t.Fatal(err)
+	}
+	if got := strings.ReplaceAll(string(content), "\r\n", "\n"); got != "hello\nnew\nbye\n" {
+		t.Fatalf("patched content = %q", got)
+	}
+}
+
+func TestStructuredHunkAnchorKeepsHeadingAndPlainContext(t *testing.T) {
+	cases := map[string]string{
+		"-12,4 +12,6":                  "",
+		"-12 +12":                      "",
+		"-12,4 +12,6 @@":               "",
+		"-12,4 +12,6 @@ func main() {": "func main() {",
+		"func main() {":                "func main() {",
+		"":                             "",
+	}
+	for input, want := range cases {
+		if got := structuredHunkAnchor(input); got != want {
+			t.Fatalf("structuredHunkAnchor(%q) = %q, want %q", input, got, want)
+		}
+	}
+}
+
+func TestStructuredPatchMarkerSpellings(t *testing.T) {
+	begin := []string{"*** Begin Patch", "*** Begin Patch ***", "***Begin Patch", "  *** Begin Patch  ", "*** Begin Patch **"}
+	for _, line := range begin {
+		if structuredPatchMarker(line) != "begin" {
+			t.Fatalf("%q must read as the begin marker", line)
+		}
+	}
+	if structuredPatchMarker("*** End Patch ***") != "end" {
+		t.Fatal("decorated end marker must read as the end marker")
+	}
+	for _, line := range []string{"*** Update File: x", "Begin Patch", "*** Begin Patchwork"} {
+		if structuredPatchMarker(line) != "" {
+			t.Fatalf("%q must not read as a marker", line)
+		}
+	}
+}
+
+func TestStructuredPatchHeaderErrorCarriesFormatHint(t *testing.T) {
+	_, err := parseStructuredPatch("--- a/x\n+++ b/x\n")
+	if err == nil || !strings.Contains(err.Error(), "*** Update File: path") {
+		t.Fatalf("header error should teach the format, got %v", err)
+	}
+}
+
+func TestApplyPatchAcceptsAbsoluteInWorkspacePaths(t *testing.T) {
+	root := t.TempDir()
+	writeTestFile(t, filepath.Join(root, "hello.txt"), "hello\nold\n")
+	absolute := filepath.Join(root, "hello.txt")
+
+	structured := strings.Join([]string{
+		"*** Begin Patch",
+		"*** Update File: " + absolute,
+		"@@",
+		" hello",
+		"-old",
+		"+structured",
+		"*** End Patch",
+		"",
+	}, "\n")
+	result := NewScopedApplyPatchTool(root, nil).Run(context.Background(), map[string]any{"patch": structured})
+	if result.Status != StatusOK {
+		t.Fatalf("absolute in-workspace structured path should apply, got %s: %s", result.Status, result.Output)
+	}
+	content, _ := os.ReadFile(absolute)
+	if got := strings.ReplaceAll(string(content), "\r\n", "\n"); got != "hello\nstructured\n" {
+		t.Fatalf("structured content = %q", got)
+	}
+	if len(result.ChangedFiles) != 1 || result.ChangedFiles[0] != "hello.txt" {
+		t.Fatalf("changed files should be workspace-relative, got %v", result.ChangedFiles)
+	}
+
+	unified := strings.Join([]string{
+		"--- " + absolute,
+		"+++ " + absolute,
+		"@@ -1,2 +1,2 @@",
+		" hello",
+		"-structured",
+		"+unified",
+		"",
+	}, "\n")
+	result = NewScopedApplyPatchTool(root, nil).Run(context.Background(), map[string]any{"patch": unified})
+	if result.Status != StatusOK {
+		t.Fatalf("absolute in-workspace unified path should apply, got %s: %s", result.Status, result.Output)
+	}
+	content, _ = os.ReadFile(absolute)
+	if got := strings.ReplaceAll(string(content), "\r\n", "\n"); got != "hello\nunified\n" {
+		t.Fatalf("unified content = %q", got)
+	}
+}
+
+func TestApplyPatchStillRejectsAbsolutePathsOutsideWorkspace(t *testing.T) {
+	root := t.TempDir()
+	outside := filepath.Join(t.TempDir(), "escape.txt")
+	writeTestFile(t, outside, "old\n")
+
+	for name, patch := range map[string]string{
+		"structured": strings.Join([]string{"*** Begin Patch", "*** Update File: " + outside, "@@", "-old", "+new", "*** End Patch", ""}, "\n"),
+		"unified":    strings.Join([]string{"--- " + outside, "+++ " + outside, "@@ -1 +1 @@", "-old", "+new", ""}, "\n"),
+	} {
+		result := NewScopedApplyPatchTool(root, nil).Run(context.Background(), map[string]any{"patch": patch})
+		if result.Status == StatusOK {
+			t.Fatalf("%s patch outside the workspace must be rejected", name)
+		}
+		if content, _ := os.ReadFile(outside); string(content) != "old\n" {
+			t.Fatalf("%s patch must not touch a file outside the workspace", name)
+		}
+	}
+}
+
+// Unified diffs are applied in-process through the same os.Root engine as
+// structured patches: git C-quoted paths with whitespace resolve to one file,
+// and the same header outside the workspace is refused before anything is
+// written.
+func TestUnifiedPatchQuotedWhitespacePaths(t *testing.T) {
+	root := t.TempDir()
+	dir := filepath.Join(root, "work tree")
+	if err := os.MkdirAll(dir, 0o755); err != nil {
+		t.Fatal(err)
+	}
+	target := filepath.Join(dir, "file.txt")
+	writeTestFile(t, target, "hello\nold\n")
+
+	quoted := func(path string) string { return strconv.Quote(path) }
+	inside := strings.Join([]string{
+		"diff --git " + quoted("a/"+filepath.ToSlash(target)) + " " + quoted("b/"+filepath.ToSlash(target)),
+		"--- " + quoted(target),
+		"+++ " + quoted(target),
+		"@@ -1,2 +1,2 @@",
+		" hello",
+		"-old",
+		"+new",
+		"",
+	}, "\n")
+	result := NewScopedApplyPatchTool(root, nil).Run(context.Background(), map[string]any{"patch": inside})
+	if result.Status != StatusOK {
+		t.Fatalf("quoted whitespace path inside the workspace should apply, got %s: %s", result.Status, result.Output)
+	}
+	content, _ := os.ReadFile(target)
+	if got := strings.ReplaceAll(string(content), "\r\n", "\n"); got != "hello\nnew\n" {
+		t.Fatalf("content = %q", got)
+	}
+	if len(result.ChangedFiles) != 1 || result.ChangedFiles[0] != "work tree/file.txt" {
+		t.Fatalf("changed files = %v", result.ChangedFiles)
+	}
+
+	outsideDir := filepath.Join(t.TempDir(), "other tree")
+	if err := os.MkdirAll(outsideDir, 0o755); err != nil {
+		t.Fatal(err)
+	}
+	outside := filepath.Join(outsideDir, "file.txt")
+	writeTestFile(t, outside, "hello\nold\n")
+	escape := strings.Join([]string{"--- " + quoted(outside), "+++ " + quoted(outside), "@@ -1,2 +1,2 @@", " hello", "-old", "+new", ""}, "\n")
+	result = NewScopedApplyPatchTool(root, nil).Run(context.Background(), map[string]any{"patch": escape})
+	if result.Status == StatusOK {
+		t.Fatal("quoted whitespace path outside the workspace must be rejected")
+	}
+	if content, _ := os.ReadFile(outside); string(content) != "hello\nold\n" {
+		t.Fatal("outside file must be untouched")
+	}
+}
+
+// A workspace path that is swapped for a symlink escaping the root — the
+// classic check-to-use attack — is refused by the os.Root engine for both
+// formats, and the outside file is never modified.
+func TestApplyPatchRefusesSymlinkEscapingWorkspace(t *testing.T) {
+	root := t.TempDir()
+	outside := filepath.Join(t.TempDir(), "secret.txt")
+	writeTestFile(t, outside, "hello\nold\n")
+	link := filepath.Join(root, "target.txt")
+	if err := os.Symlink(outside, link); err != nil {
+		t.Skipf("symlinks unavailable: %v", err)
+	}
+	for name, patch := range map[string]string{
+		"unified":    strings.Join([]string{"--- a/target.txt", "+++ b/target.txt", "@@ -1,2 +1,2 @@", " hello", "-old", "+new", ""}, "\n"),
+		"structured": strings.Join([]string{"*** Begin Patch", "*** Update File: target.txt", "@@", " hello", "-old", "+new", "*** End Patch", ""}, "\n"),
+	} {
+		result := NewScopedApplyPatchTool(root, nil).Run(context.Background(), map[string]any{"patch": patch})
+		if result.Status == StatusOK {
+			t.Fatalf("%s patch through an escaping symlink must be refused", name)
+		}
+		if content, _ := os.ReadFile(outside); string(content) != "hello\nold\n" {
+			t.Fatalf("%s patch must not modify the file outside the workspace", name)
+		}
+	}
+}
+
+func TestUnifiedPatchCreatesDeletesAndHonoursNoNewlineMarker(t *testing.T) {
+	root := t.TempDir()
+	writeTestFile(t, filepath.Join(root, "gone.txt"), "bye\n")
+	writeTestFile(t, filepath.Join(root, "keep.txt"), "a\nb\n")
+	patch := strings.Join([]string{
+		"diff --git a/new.txt b/new.txt",
+		"new file mode 100644",
+		"--- /dev/null",
+		"+++ b/new.txt",
+		"@@ -0,0 +1,2 @@",
+		"+first",
+		"+second",
+		"\\ No newline at end of file",
+		"diff --git a/gone.txt b/gone.txt",
+		"deleted file mode 100644",
+		"--- a/gone.txt",
+		"+++ /dev/null",
+		"@@ -1 +0,0 @@",
+		"-bye",
+		"--- a/keep.txt",
+		"+++ b/keep.txt",
+		"@@ -1,2 +1,2 @@",
+		" a",
+		"-b",
+		"+c",
+		"\\ No newline at end of file",
+		"",
+	}, "\n")
+	result := NewScopedApplyPatchTool(root, nil).Run(context.Background(), map[string]any{"patch": patch})
+	if result.Status != StatusOK {
+		t.Fatalf("multi-file unified patch should apply, got %s: %s", result.Status, result.Output)
+	}
+	if content, _ := os.ReadFile(filepath.Join(root, "new.txt")); string(content) != "first\nsecond" {
+		t.Fatalf("created file = %q", string(content))
+	}
+	if _, err := os.Stat(filepath.Join(root, "gone.txt")); !os.IsNotExist(err) {
+		t.Fatal("deleted file must be gone")
+	}
+	if content, _ := os.ReadFile(filepath.Join(root, "keep.txt")); string(content) != "a\nc" {
+		t.Fatalf("updated file = %q", string(content))
+	}
+	if len(result.ChangedFiles) != 3 {
+		t.Fatalf("changed files = %v", result.ChangedFiles)
+	}
+}
+
+func TestUnifiedPatchUsesRangeHintThenFallsBackToContext(t *testing.T) {
+	root := t.TempDir()
+	// Two identical blocks: the hunk's range picks the second one, which
+	// content search alone would call ambiguous.
+	writeTestFile(t, filepath.Join(root, "dup.txt"), "x\ny\nx\ny\n")
+	patch := strings.Join([]string{"--- a/dup.txt", "+++ b/dup.txt", "@@ -3,2 +3,2 @@", " x", "-y", "+z", ""}, "\n")
+	result := NewScopedApplyPatchTool(root, nil).Run(context.Background(), map[string]any{"patch": patch})
+	if result.Status != StatusOK {
+		t.Fatalf("range-hinted hunk should apply, got %s: %s", result.Status, result.Output)
+	}
+	if content, _ := os.ReadFile(filepath.Join(root, "dup.txt")); string(content) != "x\ny\nx\nz\n" {
+		t.Fatalf("content = %q", string(content))
+	}
+	// A stale range (file grew above the hunk) still applies by unique context.
+	writeTestFile(t, filepath.Join(root, "moved.txt"), "header\nhello\nold\n")
+	patch = strings.Join([]string{"--- a/moved.txt", "+++ b/moved.txt", "@@ -1,2 +1,2 @@", " hello", "-old", "+new", ""}, "\n")
+	result = NewScopedApplyPatchTool(root, nil).Run(context.Background(), map[string]any{"patch": patch})
+	if result.Status != StatusOK {
+		t.Fatalf("offset hunk should apply by context, got %s: %s", result.Status, result.Output)
+	}
+	if content, _ := os.ReadFile(filepath.Join(root, "moved.txt")); string(content) != "header\nhello\nnew\n" {
+		t.Fatalf("content = %q", string(content))
+	}
+}
+
+func TestUnifiedPatchRenameWithHunkAndRejectsBinary(t *testing.T) {
+	root := t.TempDir()
+	writeTestFile(t, filepath.Join(root, "x.txt"), "hello\nold\n")
+	rename := strings.Join([]string{
+		"diff --git a/x.txt b/y.txt",
+		"similarity index 90%",
+		"rename from x.txt",
+		"rename to y.txt",
+		"--- a/x.txt",
+		"+++ b/y.txt",
+		"@@ -1,2 +1,2 @@",
+		" hello",
+		"-old",
+		"+new",
+		"",
+	}, "\n")
+	result := NewScopedApplyPatchTool(root, nil).Run(context.Background(), map[string]any{"patch": rename})
+	if result.Status != StatusOK {
+		t.Fatalf("rename with hunk should apply, got %s: %s", result.Status, result.Output)
+	}
+	if _, err := os.Stat(filepath.Join(root, "x.txt")); !os.IsNotExist(err) {
+		t.Fatal("renamed source must be gone")
+	}
+	if content, _ := os.ReadFile(filepath.Join(root, "y.txt")); string(content) != "hello\nnew\n" {
+		t.Fatalf("renamed content = %q", string(content))
+	}
+	for name, patch := range map[string]string{
+		"binary": "diff --git a/x b/x\nBinary files a/x and b/x differ\n",
+		"empty":  "diff --git a/x b/x\n",
+	} {
+		if result := NewScopedApplyPatchTool(root, nil).Run(context.Background(), map[string]any{"patch": patch}); result.Status == StatusOK {
+			t.Fatalf("%s patch must be rejected", name)
+		}
+	}
+}
+
+func TestUnifiedPatchCopyOperation(t *testing.T) {
+	root := t.TempDir()
+	writeTestFile(t, filepath.Join(root, "src.txt"), "hello\nold\n")
+	copyPatch := func(from, to string, hunk bool) string {
+		lines := []string{"diff --git a/" + from + " b/" + to, "similarity index 90%", "copy from " + from, "copy to " + to}
+		if hunk {
+			lines = append(lines, "--- a/"+from, "+++ b/"+to, "@@ -1,2 +1,2 @@", " hello", "-old", "+new")
+		}
+		return strings.Join(append(lines, ""), "\n")
+	}
+
+	// Success: source kept, destination created with the hunk applied, and the
+	// destination inherits the source's tracker state (read whole -> whole).
+	tracker := NewFileTracker()
+	registry := NewRegistry()
+	registry.Register(NewScopedReadFileTool(root, nil))
+	registry.Register(NewScopedApplyPatchTool(root, nil))
+	opts := RunOptions{PermissionGranted: true, FileTracker: tracker}
+	if r := registry.RunWithOptions(context.Background(), "read_file", map[string]any{"path": "src.txt"}, opts); r.Status != StatusOK {
+		t.Fatalf("read: %s", r.Output)
+	}
+	result := registry.RunWithOptions(context.Background(), "apply_patch", map[string]any{"patch": copyPatch("src.txt", "dst.txt", true)}, opts)
+	if result.Status != StatusOK {
+		t.Fatalf("copy with hunk should apply, got %s: %s", result.Status, result.Output)
+	}
+	if content, _ := os.ReadFile(filepath.Join(root, "src.txt")); string(content) != "hello\nold\n" {
+		t.Fatalf("copy must keep the source, got %q", string(content))
+	}
+	if content, _ := os.ReadFile(filepath.Join(root, "dst.txt")); string(content) != "hello\nnew\n" {
+		t.Fatalf("copy destination = %q", string(content))
+	}
+	if len(result.ChangedFiles) != 2 || result.ChangedFiles[0] != "src.txt" || result.ChangedFiles[1] != "dst.txt" {
+		t.Fatalf("changed files = %v", result.ChangedFiles)
+	}
+	destination, err := filepath.EvalSymlinks(filepath.Join(root, "dst.txt"))
+	if err != nil {
+		t.Fatal(err)
+	}
+	if !tracker.SeenWhole(destination) {
+		t.Fatal("destination copied from a fully read source must be tracked as seen whole")
+	}
+	unreadSource, _ := filepath.EvalSymlinks(filepath.Join(root, "src.txt"))
+	if _, tracked := tracker.Version(unreadSource); !tracked {
+		t.Fatal("source must stay tracked after a copy")
+	}
+
+	// Failure: destination already exists — nothing is written.
+	writeTestFile(t, filepath.Join(root, "taken.txt"), "keep\n")
+	result = NewScopedApplyPatchTool(root, nil).Run(context.Background(), map[string]any{"patch": copyPatch("src.txt", "taken.txt", false)})
+	if result.Status == StatusOK || !strings.Contains(result.Output, "already exists") {
+		t.Fatalf("copy onto an existing destination must be refused, got %s: %s", result.Status, result.Output)
+	}
+	if content, _ := os.ReadFile(filepath.Join(root, "taken.txt")); string(content) != "keep\n" {
+		t.Fatal("existing destination must be untouched")
+	}
+
+	// Failure: copy onto itself.
+	result = NewScopedApplyPatchTool(root, nil).Run(context.Background(), map[string]any{"patch": copyPatch("src.txt", "src.txt", false)})
+	if result.Status == StatusOK || !strings.Contains(result.Output, "onto itself") {
+		t.Fatalf("copy onto itself must be refused, got %s: %s", result.Status, result.Output)
+	}
+}
+
+func TestUnifiedPatchRejectsOverDeclaredHunkCounts(t *testing.T) {
+	root := t.TempDir()
+	writeTestFile(t, filepath.Join(root, "a.txt"), "hello\nold\n")
+	writeTestFile(t, filepath.Join(root, "b.txt"), "x\n")
+	// "-1,3 +1,3" over-declares a two-line hunk, so without a guard the next
+	// file's ---/+++ headers would be swallowed as "-"/"+" content.
+	patch := strings.Join([]string{
+		"--- a/a.txt", "+++ b/a.txt", "@@ -1,3 +1,3 @@", " hello", "-old", "+new",
+		"--- a/b.txt", "+++ b/b.txt", "@@ -1 +1 @@", "-x", "+y", "",
+	}, "\n")
+	result := NewScopedApplyPatchTool(root, nil).Run(context.Background(), map[string]any{"patch": patch})
+	if result.Status == StatusOK || !strings.Contains(result.Output, "declared line counts") {
+		t.Fatalf("over-declared hunk must be reported as malformed, got %s: %s", result.Status, result.Output)
+	}
+	for name, want := range map[string]string{"a.txt": "hello\nold\n", "b.txt": "x\n"} {
+		if content, _ := os.ReadFile(filepath.Join(root, name)); string(content) != want {
+			t.Fatalf("%s must be untouched after a malformed patch, got %q", name, string(content))
+		}
+	}
+	// Truncated at end of input is reported the same way.
+	truncated := "--- a/a.txt\n+++ b/a.txt\n@@ -1,2 +1,2 @@\n hello\n-old\n"
+	if result := NewScopedApplyPatchTool(root, nil).Run(context.Background(), map[string]any{"patch": truncated}); result.Status == StatusOK || !strings.Contains(result.Output, "declared line counts") {
+		t.Fatalf("truncated hunk must be reported as malformed, got %s: %s", result.Status, result.Output)
+	}
+}
+
+func TestUnifiedPatchNoNewlineMarkerOnlyAfterFinalHunk(t *testing.T) {
+	root := t.TempDir()
+	writeTestFile(t, filepath.Join(root, "two.txt"), "a\nb\nc\nd\ne\nf\n")
+	// A marker after the first of two hunks describes nothing real and must
+	// not leak into the second hunk's result: the patch is rejected untouched.
+	early := strings.Join([]string{
+		"--- a/two.txt", "+++ b/two.txt",
+		"@@ -1,2 +1,2 @@", " a", "-b", "+B", "\\ No newline at end of file",
+		"@@ -5,2 +5,2 @@", " e", "-f", "+F", "",
+	}, "\n")
+	result := NewScopedApplyPatchTool(root, nil).Run(context.Background(), map[string]any{"patch": early})
+	if result.Status == StatusOK || !strings.Contains(result.Output, "must follow the last hunk") {
+		t.Fatalf("marker before a later hunk must be rejected, got %s: %s", result.Status, result.Output)
+	}
+	if content, _ := os.ReadFile(filepath.Join(root, "two.txt")); string(content) != "a\nb\nc\nd\ne\nf\n" {
+		t.Fatal("rejected patch must not modify the file")
+	}
+	// The same marker after the final hunk applies and strips the newline.
+	final := strings.Join([]string{
+		"--- a/two.txt", "+++ b/two.txt",
+		"@@ -1,2 +1,2 @@", " a", "-b", "+B",
+		"@@ -5,2 +5,2 @@", " e", "-f", "+F", "\\ No newline at end of file", "",
+	}, "\n")
+	result = NewScopedApplyPatchTool(root, nil).Run(context.Background(), map[string]any{"patch": final})
+	if result.Status != StatusOK {
+		t.Fatalf("two-hunk patch with a final marker should apply, got %s: %s", result.Status, result.Output)
+	}
+	if content, _ := os.ReadFile(filepath.Join(root, "two.txt")); string(content) != "a\nB\nc\nd\ne\nF" {
+		t.Fatalf("content = %q", string(content))
+	}
+}
+
+// A removed "-- …" line directly followed by an added "++ …" line looks like a
+// ---/+++ header pair; the boundary check must not mistake it for one.
+func TestUnifiedPatchKeepsAdjacentDashPlusContentLines(t *testing.T) {
+	root := t.TempDir()
+	writeTestFile(t, filepath.Join(root, "notes.sql"), "select 1;\n-- old comment\nselect 2;\n")
+	patch := strings.Join([]string{
+		"--- a/notes.sql", "+++ b/notes.sql",
+		"@@ -1,3 +1,3 @@", " select 1;", "--- old comment", "+++ new comment", " select 2;", "",
+	}, "\n")
+	result := NewScopedApplyPatchTool(root, nil).Run(context.Background(), map[string]any{"patch": patch})
+	if result.Status != StatusOK {
+		t.Fatalf("adjacent -- / ++ content lines must apply, got %s: %s", result.Status, result.Output)
+	}
+	if content, _ := os.ReadFile(filepath.Join(root, "notes.sql")); string(content) != "select 1;\n++ new comment\nselect 2;\n" {
+		t.Fatalf("content = %q", string(content))
+	}
+}
+
+// A unified deletion states the content it removes; it must be verified
+// against the current file before anything is deleted.
+func TestUnifiedPatchDeletionVerifiesExpectedContent(t *testing.T) {
+	deletion := func(path string, hunks ...string) string {
+		lines := []string{"diff --git a/" + path + " b/" + path, "deleted file mode 100644", "--- a/" + path, "+++ /dev/null"}
+		return strings.Join(append(append(lines, hunks...), ""), "\n")
+	}
+	t.Run("matching deletion succeeds", func(t *testing.T) {
+		root := t.TempDir()
+		writeTestFile(t, filepath.Join(root, "gone.txt"), "current\n")
+		result := NewScopedApplyPatchTool(root, nil).Run(context.Background(), map[string]any{"patch": deletion("gone.txt", "@@ -1 +0,0 @@", "-current")})
+		if result.Status != StatusOK {
+			t.Fatalf("matching deletion should apply, got %s: %s", result.Status, result.Output)
+		}
+		if _, err := os.Stat(filepath.Join(root, "gone.txt")); !os.IsNotExist(err) {
+			t.Fatal("file must be deleted")
+		}
+	})
+	t.Run("stale deletion is refused untouched", func(t *testing.T) {
+		root := t.TempDir()
+		writeTestFile(t, filepath.Join(root, "gone.txt"), "current\n")
+		result := NewScopedApplyPatchTool(root, nil).Run(context.Background(), map[string]any{"patch": deletion("gone.txt", "@@ -1 +0,0 @@", "-stale")})
+		if result.Status == StatusOK || !strings.Contains(result.Output, "does not match its current content") {
+			t.Fatalf("stale deletion must be refused, got %s: %s", result.Status, result.Output)
+		}
+		if content, _ := os.ReadFile(filepath.Join(root, "gone.txt")); string(content) != "current\n" {
+			t.Fatalf("file must be byte-for-byte unchanged, got %q", string(content))
+		}
+	})
+	t.Run("partial deletion is refused", func(t *testing.T) {
+		root := t.TempDir()
+		writeTestFile(t, filepath.Join(root, "gone.txt"), "one\ntwo\n")
+		result := NewScopedApplyPatchTool(root, nil).Run(context.Background(), map[string]any{"patch": deletion("gone.txt", "@@ -1 +0,0 @@", "-one")})
+		if result.Status == StatusOK || !strings.Contains(result.Output, "does not match its current content") {
+			t.Fatalf("deletion that does not cover the file must be refused, got %s: %s", result.Status, result.Output)
+		}
+		if content, _ := os.ReadFile(filepath.Join(root, "gone.txt")); string(content) != "one\ntwo\n" {
+			t.Fatal("file must be unchanged")
+		}
+	})
+	t.Run("header-only deletion is refused", func(t *testing.T) {
+		root := t.TempDir()
+		writeTestFile(t, filepath.Join(root, "gone.txt"), "current\n")
+		result := NewScopedApplyPatchTool(root, nil).Run(context.Background(), map[string]any{"patch": deletion("gone.txt")})
+		if result.Status == StatusOK || !strings.Contains(result.Output, "must include the hunk") {
+			t.Fatalf("header-only deletion must be refused, got %s: %s", result.Status, result.Output)
+		}
+		if _, err := os.Stat(filepath.Join(root, "gone.txt")); err != nil {
+			t.Fatal("file must still exist")
+		}
+	})
+	t.Run("multi-hunk deletion verifies everything before removing", func(t *testing.T) {
+		root := t.TempDir()
+		writeTestFile(t, filepath.Join(root, "gone.txt"), "a\nb\nc\nd\n")
+		good := deletion("gone.txt", "@@ -1,2 +0,0 @@", "-a", "-b", "@@ -3,2 +0,0 @@", "-c", "-d")
+		bad := deletion("gone.txt", "@@ -1,2 +0,0 @@", "-a", "-b", "@@ -3,2 +0,0 @@", "-c", "-stale")
+		result := NewScopedApplyPatchTool(root, nil).Run(context.Background(), map[string]any{"patch": bad})
+		if result.Status == StatusOK {
+			t.Fatalf("deletion with one stale hunk must be refused: %s", result.Output)
+		}
+		if content, _ := os.ReadFile(filepath.Join(root, "gone.txt")); string(content) != "a\nb\nc\nd\n" {
+			t.Fatal("no hunk may be applied when any hunk is stale")
+		}
+		result = NewScopedApplyPatchTool(root, nil).Run(context.Background(), map[string]any{"patch": good})
+		if result.Status != StatusOK {
+			t.Fatalf("multi-hunk deletion should apply, got %s: %s", result.Status, result.Output)
+		}
+		if _, err := os.Stat(filepath.Join(root, "gone.txt")); !os.IsNotExist(err) {
+			t.Fatal("file must be deleted")
+		}
+	})
+	t.Run("structured delete stays unconditional", func(t *testing.T) {
+		root := t.TempDir()
+		writeTestFile(t, filepath.Join(root, "gone.txt"), "anything\n")
+		patch := "*** Begin Patch\n*** Delete File: gone.txt\n*** End Patch\n"
+		if result := NewScopedApplyPatchTool(root, nil).Run(context.Background(), map[string]any{"patch": patch}); result.Status != StatusOK {
+			t.Fatalf("structured delete should apply, got %s: %s", result.Status, result.Output)
+		}
+	})
+}
+
+// The source is re-read through the root immediately before commit, so a
+// change made after planning is refused instead of overwritten or removed.
+func TestApplyStructuredPatchChangeRefusesSourceChangedAfterPlanning(t *testing.T) {
+	root := t.TempDir()
+	path := filepath.Join(root, "file.txt")
+	writeTestFile(t, path, "planned\n")
+	workspace, err := os.OpenRoot(root)
+	if err != nil {
+		t.Fatal(err)
+	}
+	defer workspace.Close()
+	target := structuredPatchTarget{requested: "file.txt", absolute: path, relative: "file.txt"}
+	destination := structuredPatchTarget{requested: "copy.txt", absolute: filepath.Join(root, "copy.txt"), relative: "copy.txt"}
+	for name, change := range map[string]structuredPatchChange{
+		"update": {kind: structuredPatchUpdate, from: target, to: target, before: "planned\n", after: "new\n", mode: 0o644},
+		"delete": {kind: structuredPatchDelete, from: target, to: target, before: "planned\n", mode: 0o644},
+		"copy":   {kind: structuredPatchCopy, from: target, to: destination, before: "planned\n", after: "planned\n", mode: 0o644},
+	} {
+		writeTestFile(t, path, "changed after planning\n")
+		committed, err := applyStructuredPatchChange(workspace, change)
+		if err == nil || committed || !strings.Contains(err.Error(), "changed on disk between planning and commit") {
+			t.Fatalf("%s: expected a refusal, got committed=%v err=%v", name, committed, err)
+		}
+		if content, _ := os.ReadFile(path); string(content) != "changed after planning\n" {
+			t.Fatalf("%s: file must be untouched, got %q", name, string(content))
+		}
+		if _, statErr := os.Stat(filepath.Join(root, "copy.txt")); !os.IsNotExist(statErr) {
+			t.Fatalf("%s: refused change must not create copy.txt", name)
+		}
+	}
+}
+
+func TestUnifiedPatchDeletionIsByteExact(t *testing.T) {
+	deletion := func(hunks ...string) string {
+		return strings.Join(append(append([]string{"--- a/gone.txt", "+++ /dev/null"}, hunks...), ""), "\n")
+	}
+	for name, tc := range map[string]struct{ file, patch string }{
+		"trailing whitespace differs": {"current  \n", deletion("@@ -1 +0,0 @@", "-current")},
+		"indentation differs":         {"  current\n", deletion("@@ -1 +0,0 @@", "-current")},
+		"blank line not covered":      {"current\n\n", deletion("@@ -1 +0,0 @@", "-current")},
+		"space-only line not covered": {"current\n   \n", deletion("@@ -1 +0,0 @@", "-current")},
+		"missing final newline":       {"current", deletion("@@ -1 +0,0 @@", "-current")},
+	} {
+		t.Run(name, func(t *testing.T) {
+			root := t.TempDir()
+			writeTestFile(t, filepath.Join(root, "gone.txt"), tc.file)
+			result := NewScopedApplyPatchTool(root, nil).Run(context.Background(), map[string]any{"patch": tc.patch})
+			if result.Status == StatusOK {
+				t.Fatalf("deletion must be byte-exact; %q was deleted by a non-matching hunk", tc.file)
+			}
+			if content, _ := os.ReadFile(filepath.Join(root, "gone.txt")); string(content) != tc.file {
+				t.Fatalf("file must be unchanged, got %q", string(content))
+			}
+		})
+	}
+	t.Run("no-newline marker on the removed side matches exactly", func(t *testing.T) {
+		root := t.TempDir()
+		writeTestFile(t, filepath.Join(root, "gone.txt"), "current")
+		patch := deletion("@@ -1 +0,0 @@", "-current", "\\ No newline at end of file")
+		if result := NewScopedApplyPatchTool(root, nil).Run(context.Background(), map[string]any{"patch": patch}); result.Status != StatusOK {
+			t.Fatalf("deletion with a matching no-newline marker should apply, got %s: %s", result.Status, result.Output)
+		}
+		if _, err := os.Stat(filepath.Join(root, "gone.txt")); !os.IsNotExist(err) {
+			t.Fatal("file must be deleted")
+		}
+	})
+	t.Run("CRLF file matches an LF patch of the same content", func(t *testing.T) {
+		root := t.TempDir()
+		writeTestFile(t, filepath.Join(root, "gone.txt"), "a\r\nb\r\n")
+		if result := NewScopedApplyPatchTool(root, nil).Run(context.Background(), map[string]any{"patch": deletion("@@ -1,2 +0,0 @@", "-a", "-b")}); result.Status != StatusOK {
+			t.Fatalf("CRLF deletion should apply, got %s: %s", result.Status, result.Output)
+		}
+	})
+}
+
+// git describes an empty file's creation or deletion with header lines only.
+func TestUnifiedPatchHeaderOnlyEmptyFileForms(t *testing.T) {
+	root := t.TempDir()
+	writeTestFile(t, filepath.Join(root, "empty.txt"), "")
+	writeTestFile(t, filepath.Join(root, "full.txt"), "content\n")
+	writeTestFile(t, filepath.Join(root, "keep.txt"), "a\n")
+	deleteHeader := func(path string) string {
+		return "diff --git a/" + path + " b/" + path + "\ndeleted file mode 100644\nindex e69de29..0000000\n"
+	}
+	// A non-empty file is not deleted by the header-only form.
+	result := NewScopedApplyPatchTool(root, nil).Run(context.Background(), map[string]any{"patch": deleteHeader("full.txt")})
+	if result.Status == StatusOK || !strings.Contains(result.Output, "expects an empty file") {
+		t.Fatalf("header-only deletion of a non-empty file must be refused, got %s: %s", result.Status, result.Output)
+	}
+	if _, err := os.Stat(filepath.Join(root, "full.txt")); err != nil {
+		t.Fatal("non-empty file must still exist")
+	}
+	// In a multi-file patch the empty-file deletion and creation are applied
+	// alongside a normal hunk.
+	patch := deleteHeader("empty.txt") +
+		"diff --git a/blank.txt b/blank.txt\nnew file mode 100644\nindex 0000000..e69de29\n" +
+		"diff --git a/keep.txt b/keep.txt\n--- a/keep.txt\n+++ b/keep.txt\n@@ -1 +1 @@\n-a\n+b\n"
+	result = NewScopedApplyPatchTool(root, nil).Run(context.Background(), map[string]any{"patch": patch})
+	if result.Status != StatusOK {
+		t.Fatalf("multi-file patch with header-only forms should apply, got %s: %s", result.Status, result.Output)
+	}
+	if _, err := os.Stat(filepath.Join(root, "empty.txt")); !os.IsNotExist(err) {
+		t.Fatal("empty file must be deleted")
+	}
+	if content, err := os.ReadFile(filepath.Join(root, "blank.txt")); err != nil || len(content) != 0 {
+		t.Fatalf("empty file must be created, got err=%v content=%q", err, string(content))
+	}
+	if content, _ := os.ReadFile(filepath.Join(root, "keep.txt")); string(content) != "b\n" {
+		t.Fatalf("hunk file = %q", string(content))
+	}
+	if len(result.ChangedFiles) != 3 {
+		t.Fatalf("changed files = %v", result.ChangedFiles)
+	}
+}
+
+// When a later change fails, the error names exactly which files were already
+// committed so the caller knows what changed and what did not.
+func TestApplyPatchOperationsReportsCommittedPrefixOnFailure(t *testing.T) {
+	root := t.TempDir()
+	writeTestFile(t, filepath.Join(root, "first.txt"), "one\n")
+	writeTestFile(t, filepath.Join(root, "second.txt"), "two\n")
+	writeTestFile(t, filepath.Join(root, "third.txt"), "three\n")
+	// Make second.txt change after planning so its commit is refused.
+	structuredPatchBeforeCommit = func(change structuredPatchChange) {
+		if change.to.relative == "second.txt" {
+			writeTestFile(t, filepath.Join(root, "second.txt"), "changed\n")
+		}
+	}
+	defer func() { structuredPatchBeforeCommit = nil }()
+	patch := strings.Join([]string{
+		"*** Begin Patch",
+		"*** Update File: first.txt", "@@", "-one", "+ONE",
+		"*** Update File: second.txt", "@@", "-two", "+TWO",
+		"*** Update File: third.txt", "@@", "-three", "+THREE",
+		"*** End Patch", "",
+	}, "\n")
+	result := NewScopedApplyPatchTool(root, nil).Run(context.Background(), map[string]any{"patch": patch})
+	if result.Status == StatusOK {
+		t.Fatal("patch must fail when a later change is refused")
+	}
+	for _, want := range []string{"already committed: first.txt", "remaining files are unchanged"} {
+		if !strings.Contains(result.Output, want) {
+			t.Fatalf("error must report the committed prefix, got: %s", result.Output)
+		}
+	}
+	if strings.Contains(result.Output, "committed: first.txt, second.txt") || strings.Contains(result.Output, "third.txt") {
+		t.Fatalf("error must not list uncommitted files as committed: %s", result.Output)
+	}
+	if content, _ := os.ReadFile(filepath.Join(root, "first.txt")); string(content) != "ONE\n" {
+		t.Fatalf("first.txt must hold the committed change, got %q", string(content))
+	}
+	if content, _ := os.ReadFile(filepath.Join(root, "second.txt")); string(content) != "changed\n" {
+		t.Fatalf("second.txt must be untouched by the patch, got %q", string(content))
+	}
+	if content, _ := os.ReadFile(filepath.Join(root, "third.txt")); string(content) != "three\n" {
+		t.Fatalf("third.txt must be untouched, got %q", string(content))
+	}
+}

internal/tools/edit_file.go

@@ -168,7 +168,7 @@ func (tool editFileTool) RunWithOptions(ctx context.Context, args map[string]any
 	options.FileTracker.Record(absolutePath, []byte(updated), newInfo)
 	if updated == modelKnownContent {
 		if previouslySeenWhole {
-			options.FileTracker.RecordSeenRange(absolutePath, 1, lineCount(updated), lineCount(updated))
+			options.FileTracker.RecordSeenRange(absolutePath, 1, trackedLineTotal(updated), trackedLineTotal(updated))
 		} else {
 			for _, span := range editedSpans {
 				options.FileTracker.RecordSeenBytes(absolutePath, span.start, span.end, len(updated))

internal/tools/file_tools_test.go

@@ -26,8 +26,8 @@ func TestReadFileToolReadsLineRanges(t *testing.T) {
 	}
 	for _, want := range []string{
 		"File: notes.txt (lines 2-3 of 4)",
-		"2 | beta",
-		"3 | gamma",
+		"2→beta",
+		"3→gamma",
 	} {
 		if !strings.Contains(result.Output, want) {
 			t.Fatalf("expected output to contain %q, got %q", want, result.Output)
@@ -54,7 +54,7 @@ func TestReadFileToolReadsCanonicalLineRange(t *testing.T) {
 	if result.Truncated {
 		t.Fatalf("canonical limit defines the requested range and must not mark it truncated: %#v", result.Meta)
 	}
-	if !strings.Contains(result.Output, "2 | beta") || !strings.Contains(result.Output, "3 | gamma") {
+	if !strings.Contains(result.Output, "2→beta") || !strings.Contains(result.Output, "3→gamma") {
 		t.Fatalf("canonical range returned the wrong lines: %q", result.Output)
 	}
 	if strings.Contains(result.Output, "alpha") || strings.Contains(result.Output, "delta") {
@@ -94,7 +94,7 @@ func TestReadFileToolMixedLegacyRangesPreferLines(t *testing.T) {
 	if result.Status != StatusOK {
 		t.Fatalf("mixed legacy range should recover, got %s: %s", result.Status, result.Output)
 	}
-	if !strings.Contains(result.Output, "2 | beta") || !strings.Contains(result.Output, "3 | gamma") {
+	if !strings.Contains(result.Output, "2→beta") || !strings.Contains(result.Output, "3→gamma") {
 		t.Fatalf("mixed legacy range did not prefer lines: %q", result.Output)
 	}
 }
@@ -110,7 +110,7 @@ func TestReadFileToolCombinesLegacyStartWithCanonicalLimit(t *testing.T) {
 	if result.Status != StatusOK || result.Truncated {
 		t.Fatalf("mixed compatible range should be exact, got status=%s truncated=%v: %s", result.Status, result.Truncated, result.Output)
 	}
-	if !strings.Contains(result.Output, "2 | beta") || !strings.Contains(result.Output, "3 | gamma") {
+	if !strings.Contains(result.Output, "2→beta") || !strings.Contains(result.Output, "3→gamma") {
 		t.Fatalf("mixed compatible range returned the wrong lines: %q", result.Output)
 	}
 	if strings.Contains(result.Output, "alpha") || strings.Contains(result.Output, "delta") {
@@ -955,7 +955,7 @@ func TestReadFileToolRecoversBackwardsRange(t *testing.T) {
 	for _, want := range []string{
 		"end_line 2 was before start_line 3", // the note
 		"only line 3 was read",
-		"3 | gamma",
+		"3→gamma",
 	} {
 		if !strings.Contains(result.Output, want) {
 			t.Fatalf("expected %q in output, got %q", want, result.Output)
@@ -984,7 +984,7 @@ func TestReadFileToolValidRangeUnchangedByRecovery(t *testing.T) {
 	// Byte-for-byte: header, blank separator, the exact selected lines, and no
 	// recovery note or trailing content. An altered header/separator or a stray
 	// out-of-range line would fail this where a substring check would not.
-	const want = "File: notes.txt (lines 2-4 of 5)\n\n2 | beta\n3 | gamma\n4 | delta"
+	const want = "File: notes.txt (lines 2-4 of 5)\n\n2→beta\n3→gamma\n4→delta"
 	if result.Output != want {
 		t.Fatalf("valid-range output changed by the recovery path:\n got: %q\nwant: %q", result.Output, want)
 	}

internal/tools/model_visibility.go

@@ -1,9 +1,11 @@
 package tools
 
 // ModelVisible reports whether a registered tool is advertised to an agent.
-// edit_file remains implemented for compatibility with existing integrations,
-// but its text-only replacement contract cannot safely disambiguate repeated
-// source fragments. Agents use apply_patch for contextual existing-file edits.
+// Every registered tool is visible. edit_file (exact search/replace with a
+// uniqueness guard, CRLF and fuzzy fallbacks) was hidden for a while in favour
+// of apply_patch; head-to-head benchmarking showed that when a model misses the
+// patch grammar it degrades to whole-file rewrites, so both edit tools are
+// advertised and the prompt steers between them.
 func ModelVisible(tool Tool) bool {
-	return tool != nil && tool.Name() != "edit_file"
+	return tool != nil
 }

internal/tools/model_visibility_test.go

@@ -2,17 +2,28 @@ package tools
 
 import "testing"
 
-func TestToolSearchDoesNotSurfaceLegacyStringReplacement(t *testing.T) {
+func TestToolSearchSurfacesBothEditTools(t *testing.T) {
 	registry := NewRegistry()
 	registry.Register(NewScopedEditFileTool(t.TempDir(), nil))
 	registry.Register(NewScopedApplyPatchTool(t.TempDir(), nil))
 	search := NewToolSearchTool(registry).(toolSearchTool)
 
 	eager := search.visibleEagerToolNames(nil, nil, "ask")
-	if eager["edit_file"] {
-		t.Fatal("tool_search must not describe edit_file as available to the model")
+	if !eager["edit_file"] {
+		t.Fatal("tool_search must describe edit_file as available to the model")
 	}
 	if !eager["apply_patch"] {
-		t.Fatal("tool_search must retain apply_patch as the available edit tool")
+		t.Fatal("tool_search must retain apply_patch as an available edit tool")
+	}
+}
+
+func TestModelVisibleAdvertisesEveryRegisteredTool(t *testing.T) {
+	if ModelVisible(nil) {
+		t.Fatal("a nil tool must not be visible")
+	}
+	for _, tool := range []Tool{NewScopedEditFileTool(t.TempDir(), nil), NewScopedApplyPatchTool(t.TempDir(), nil), NewScopedWriteFileTool(t.TempDir(), nil)} {
+		if !ModelVisible(tool) {
+			t.Fatalf("%s must be visible to the model", tool.Name())
+		}
 	}
 }

internal/tools/read_file.go

@@ -9,12 +9,14 @@ import (
 	"io"
 	"os"
 	"strconv"
-	"strings"
 	"unicode/utf8"
 )
 
 const readFileByteChunkMax = 64 * 1024
 
+// readFileLinePrefixSeparator follows the line number on every read_file line.
+const readFileLinePrefixSeparator = "→"
+
 type readFileTool struct {
 	baseTool
 	workspaceRoot string
@@ -31,7 +33,7 @@ func NewScopedReadFileTool(workspaceRoot string, scope PathScope) Tool {
 	return readFileTool{
 		baseTool: baseTool{
 			name:        "read_file",
-			description: "Read exact file text with line numbers. Use for comments, formatting, or edits; prefer read_minified_file for initial code understanding. Use offset and limit for a line range.",
+			description: "Read exact file text, each line prefixed with its line number and →. Use for comments, formatting, or edits; prefer read_minified_file for initial code understanding. Use offset and limit for a line range.",
 			parameters: Schema{
 				Type: "object",
 				Properties: map[string]PropertySchema{
@@ -221,7 +223,6 @@ func renderReadFileRange(absolutePath string, relativePath string, total int, st
 	}
 
 	lastLine := startLine + selectedLines - 1
-	width := len(strconv.Itoa(lastLine))
 	header := fmt.Sprintf("File: %s (%d lines)", relativePath, total)
 	if startLine != 1 || endLine != total || maxLines > 0 {
 		header = fmt.Sprintf("File: %s (lines %d-%d of %d)", relativePath, startLine, lastLine, total)
@@ -244,7 +245,7 @@ func renderReadFileRange(absolutePath string, relativePath string, total int, st
 		budgetedOutput.WriteString("\n")
 	}
 	budgetedOutput.WriteString("\n")
-	if err := appendReadFileRange(budgetedOutput, absolutePath, startLine, selectedLines, width); err != nil {
+	if err := appendReadFileRange(budgetedOutput, absolutePath, startLine, selectedLines); err != nil {
 		return errorResult("Error reading file " + relativePath + ": " + err.Error())
 	}
 	if truncated {
@@ -357,7 +358,7 @@ func renderReadFileBytes(path, relativePath string, total, requestedStart, limit
 	return Result{Status: StatusOK, Output: output, Meta: map[string]string{"next_byte_offset": strconv.Itoa(end)}}, start, end
 }
 
-func appendReadFileRange(output *outputBudgetBuilder, path string, startLine int, selectedLines int, width int) error {
+func appendReadFileRange(output *outputBudgetBuilder, path string, startLine int, selectedLines int) error {
 	file, err := os.Open(path)
 	if err != nil {
 		return err
@@ -380,10 +381,11 @@ func appendReadFileRange(output *outputBudgetBuilder, path string, startLine int
 			if emitted > 0 {
 				output.WriteString("\n")
 			}
-			number := strconv.Itoa(lineNumber)
-			output.WriteString(strings.Repeat(" ", width-len(number)))
-			output.WriteString(number)
-			output.WriteString(" | ")
+			// Compact "N→" prefix: the padded "  N | " form cost ~19% of every
+			// read (about 1.5k tokens per 800-line file) and was re-sent on each
+			// later call; no consumer parses it, and models read "N→" natively.
+			output.WriteString(strconv.Itoa(lineNumber))
+			output.WriteString(readFileLinePrefixSeparator)
 			output.WriteString(string(trimLineBreak(raw, ended)))
 			emitted++
 		}

internal/tools/read_minified_file.go

@@ -171,14 +171,9 @@ func selectSourceLines(content []byte, offset, limit int) sourceSelection {
 }
 
 func sourceLineCount(content []byte) int {
-	if len(content) == 0 {
-		return 1
-	}
-	lines := strings.Count(string(content), "\n")
-	if content[len(content)-1] != '\n' {
-		lines++
-	}
-	return lines
+	// One implementation for reader and writer: the tracker contract lives on
+	// trackedLineTotal, and this must never drift from it.
+	return trackedLineTotal(string(content))
 }
 
 // lineCount reports the number of newline-separated lines in s (an empty string
@@ -189,3 +184,20 @@ func lineCount(s string) int {
 	}
 	return strings.Count(s, "\n") + 1
 }
+
+// trackedLineTotal reports a file's line count the way read_file reports it
+// to the FileTracker (newline-terminated lines, plus an unterminated last
+// line; an empty file is one line). Writers must record this same number:
+// RecordSeenRange resets every observation when the total changes, so a
+// writer that recorded lineCount (one higher for a trailing newline) made the
+// next partial read_file wipe whole-file knowledge and refuse the next edit.
+func trackedLineTotal(s string) int {
+	if s == "" {
+		return 1
+	}
+	total := strings.Count(s, "\n")
+	if !strings.HasSuffix(s, "\n") {
+		total++
+	}
+	return total
+}

internal/tools/structured_patch.go

@@ -6,9 +6,11 @@ import (
 	"io"
 	"os"
 	"path/filepath"
+	"regexp"
 	"strings"
 
 	"github.com/Gitlawb/zero/internal/pathjail"
+	"github.com/Gitlawb/zero/internal/sandbox"
 )
 
 const (
@@ -28,6 +30,9 @@ const (
 	structuredPatchAdd structuredPatchKind = iota
 	structuredPatchDelete
 	structuredPatchUpdate
+	// structuredPatchCopy creates movePath from path's content (plus any
+	// hunks) and keeps path; produced by a unified diff's "copy from/to".
+	structuredPatchCopy
 )
 
 type structuredPatchOperation struct {
@@ -37,8 +42,29 @@ type structuredPatchOperation struct {
 	contents string
 	chunks   []structuredPatchChunk
 	line     int
+	// eofNewline lets a unified diff's "\ No newline at end of file" marker
+	// force the trailing-newline state of the result; structured patches keep
+	// the file's existing state.
+	eofNewline eofNewlineMode
+	// verifyDelete marks a deletion that carries the expected old content
+	// (a unified diff's "+++ /dev/null" hunks, or git's header-only form for
+	// an empty file): the removed lines must equal the current file byte for
+	// byte, otherwise the deletion is stale and refused. A structured
+	// "*** Delete File" means "delete this path" and has no chunks.
+	verifyDelete bool
+	// oldNoNewline records a unified diff's "\ No newline at end of file"
+	// on the removed side, i.e. the old content did not end with a newline.
+	oldNoNewline bool
 }
 
+type eofNewlineMode uint8
+
+const (
+	eofNewlineKeep eofNewlineMode = iota
+	eofNewlinePresent
+	eofNewlineAbsent
+)
+
 type structuredPatchChunk struct {
 	context          string
 	hasContext       bool
@@ -46,6 +72,11 @@ type structuredPatchChunk struct {
 	new              []string
 	newSourceOffsets []int
 	endOfFile        bool
+	// hint is the 0-based line the hunk is expected at (from a unified diff's
+	// "@@ -a,b" range). When the expected lines match there it is used as-is;
+	// otherwise the hunk is located by content like a structured hunk.
+	hint    int
+	hasHint bool
 }
 
 type structuredPatchTarget struct {
@@ -63,8 +94,36 @@ type structuredPatchChange struct {
 	mode   os.FileMode
 }
 
+// unifiedHunkRangePattern recognises a unified-diff range header ("-12,4 +12,6",
+// optionally followed by "@@ heading") written inside a structured hunk marker.
+// The line numbers carry no information for the context-anchored grammar, so
+// the range is dropped and only an explicit heading is kept as the anchor.
+var unifiedHunkRangePattern = regexp.MustCompile(`^-\d+(?:,\d+)?\s+\+\d+(?:,\d+)?\s*(?:@@\s*(.*))?$`)
+
+const structuredPatchFormatHint = ` (format: "*** Begin Patch", then "*** Update File: path" / "*** Add File: path" / "*** Delete File: path" sections whose hunks start with "@@" and use " " context, "-" removed and "+" added lines, then "*** End Patch")`
+
+// structuredPatchMarker classifies a line as the "begin" or "end" marker of a
+// structured patch, or "" when it is neither. The classifier is owned by the
+// sandbox package so the boundary check and the tool accept exactly the same
+// spellings; a strict byte-equal match here once made every patch from some
+// models fail on line 1 and pushed them into whole-file rewrites.
+func structuredPatchMarker(line string) string {
+	return sandbox.StructuredPatchMarker(line)
+}
+
+// structuredHunkAnchor normalises the text after a hunk's "@@ " marker. A
+// unified-diff range is dropped (its optional heading survives as the anchor);
+// anything else is used verbatim.
+func structuredHunkAnchor(context string) string {
+	context = strings.TrimSpace(context)
+	if match := unifiedHunkRangePattern.FindStringSubmatch(context); match != nil {
+		return strings.TrimSpace(match[1])
+	}
+	return context
+}
+
 func isStructuredPatch(patch string) bool {
-	return strings.HasPrefix(strings.TrimSpace(strings.TrimPrefix(patch, "\ufeff")), structuredPatchBegin)
+	return sandbox.IsStructuredPatch(patch)
 }
 
 func (tool applyPatchTool) runStructuredPatch(applyRoot, relativeRoot, patch string, options RunOptions) Result {
@@ -72,6 +131,14 @@ func (tool applyPatchTool) runStructuredPatch(applyRoot, relativeRoot, patch str
 	if err != nil {
 		return errorResult("Error applying patch: " + err.Error())
 	}
+	return applyPatchOperations(applyRoot, relativeRoot, operations, options)
+}
+
+// applyPatchOperations applies parsed operations (from either patch format)
+// through an opened workspace root: every stat, read, create and write is
+// descriptor-relative and refuses to follow a link out of the root, so there
+// is no pathname check-to-use window between validation and write.
+func applyPatchOperations(applyRoot, relativeRoot string, operations []structuredPatchOperation, options RunOptions) Result {
 	workspace, err := os.OpenRoot(applyRoot)
 	if err != nil {
 		return errorResult("Error applying patch: " + err.Error())
@@ -84,7 +151,7 @@ func (tool applyPatchTool) runStructuredPatch(applyRoot, relativeRoot, patch str
 	wholeBefore := make(map[string]bool, len(changes))
 	if options.FileTracker != nil {
 		for _, change := range changes {
-			if change.kind == structuredPatchUpdate {
+			if change.kind == structuredPatchUpdate || change.kind == structuredPatchCopy {
 				wholeBefore[change.from.absolute] = options.FileTracker.SeenWhole(change.from.absolute)
 			}
 		}
@@ -103,6 +170,10 @@ func (tool applyPatchTool) runStructuredPatch(applyRoot, relativeRoot, patch str
 			wasWhole := wholeBefore[change.from.absolute]
 			options.FileTracker.Forget(change.from.absolute)
 			recordStructuredPatchFile(options.FileTracker, change.to.absolute, false, wasWhole)
+		case structuredPatchCopy:
+			// The source is untouched; the destination inherits only what the
+			// model had actually seen of the source.
+			recordStructuredPatchFile(options.FileTracker, change.to.absolute, true, wholeBefore[change.from.absolute])
 		}
 	}
 
@@ -122,11 +193,11 @@ func parseStructuredPatch(patch string) ([]structuredPatchOperation, error) {
 		return nil, fmt.Errorf("structured patch is empty")
 	}
 	lines := strings.Split(normalized, "\n")
-	if strings.TrimSpace(lines[0]) != structuredPatchBegin {
-		return nil, fmt.Errorf("the first line of a structured patch must be %q", structuredPatchBegin)
+	if structuredPatchMarker(lines[0]) != "begin" {
+		return nil, fmt.Errorf("the first line of a structured patch must be %q%s", structuredPatchBegin, structuredPatchFormatHint)
 	}
-	if strings.TrimSpace(lines[len(lines)-1]) != structuredPatchEnd {
-		return nil, fmt.Errorf("the last line of a structured patch must be %q", structuredPatchEnd)
+	if structuredPatchMarker(lines[len(lines)-1]) != "end" {
+		return nil, fmt.Errorf("the last line of a structured patch must be %q%s", structuredPatchEnd, structuredPatchFormatHint)
 	}
 
 	var operations []structuredPatchOperation
@@ -191,8 +262,12 @@ func parseStructuredPatch(patch string) ([]structuredPatchOperation, error) {
 				}
 				if trimmed == "@@" || strings.HasPrefix(trimmed, structuredHunkContext) {
 					chunk := structuredPatchChunk{}
+					rest := ""
 					if trimmed != "@@" {
-						chunk.context = strings.TrimPrefix(trimmed, structuredHunkContext)
+						rest = strings.TrimPrefix(trimmed, structuredHunkContext)
+					}
+					if anchor := structuredHunkAnchor(rest); anchor != "" {
+						chunk.context = anchor
 						chunk.hasContext = true
 					}
 					op.chunks = append(op.chunks, chunk)
@@ -248,7 +323,7 @@ func structuredPatchPath(header, prefix string, line int) (string, error) {
 }
 
 func isStructuredPatchHeader(line string) bool {
-	return line == structuredPatchEnd || strings.HasPrefix(line, structuredAddFile) || strings.HasPrefix(line, structuredDeleteFile) || strings.HasPrefix(line, structuredUpdateFile)
+	return structuredPatchMarker(line) == "end" || strings.HasPrefix(line, structuredAddFile) || strings.HasPrefix(line, structuredDeleteFile) || strings.HasPrefix(line, structuredUpdateFile)
 }
 
 func structuredPatchLineError(line int, message string) error {
@@ -318,7 +393,7 @@ func planStructuredPatch(root *os.Root, operations []structuredPatchOperation, t
 				return nil, err
 			}
 			change.after = operation.contents
-		case structuredPatchDelete, structuredPatchUpdate:
+		case structuredPatchDelete, structuredPatchUpdate, structuredPatchCopy:
 			info, err := root.Stat(from.relative)
 			if err != nil {
 				return nil, fmt.Errorf("stating %s: %w", from.relative, err)
@@ -332,12 +407,20 @@ func planStructuredPatch(root *os.Root, operations []structuredPatchOperation, t
 				return nil, fmt.Errorf("%s", fileConflictMessage(from.relative))
 			}
 			change.before = string(content)
-			if operation.kind == structuredPatchUpdate {
+			if operation.kind == structuredPatchDelete && operation.verifyDelete {
+				if err := verifyUnifiedDeletion(change.before, from.relative, operation); err != nil {
+					return nil, err
+				}
+			}
+			if operation.kind == structuredPatchUpdate || operation.kind == structuredPatchCopy {
 				updated, err := applyStructuredPatchUpdate(change.before, from.relative, operation.chunks)
 				if err != nil {
 					return nil, err
 				}
-				change.after = updated
+				change.after = applyEOFNewline(updated, operation.eofNewline)
+				if operation.kind == structuredPatchCopy && from.absolute == to.absolute {
+					return nil, fmt.Errorf("cannot copy %s onto itself", from.relative)
+				}
 				if from.absolute != to.absolute {
 					if _, err := root.Lstat(to.relative); err == nil {
 						return nil, fmt.Errorf("cannot move %s to %s because the destination already exists", from.relative, to.relative)
@@ -353,10 +436,14 @@ func planStructuredPatch(root *os.Root, operations []structuredPatchOperation, t
 }
 
 func resolveStructuredPatchTarget(root, path string) (structuredPatchTarget, error) {
-	if filepath.IsAbs(path) || path == ".." || strings.HasPrefix(filepath.ToSlash(path), "../") {
+	// Relative traversal is rejected outright. An absolute path is allowed when
+	// it resolves inside the apply root (models routinely echo the absolute path
+	// they were shown by read_file); resolveWorkspaceTargetPath rejects anything
+	// that lands outside.
+	if path == ".." || strings.HasPrefix(filepath.ToSlash(path), "../") {
 		return structuredPatchTarget{}, fmt.Errorf("patch path %q must stay inside the workspace", path)
 	}
-	absolute, relative, err := resolveWorkspaceTargetPath(root, path)
+	absolute, relative, err := resolveWorkspaceTargetPath(root, normalizePatchPathForRoot(root, path))
 	if err != nil {
 		return structuredPatchTarget{}, err
 	}
@@ -389,9 +476,15 @@ func applyStructuredPatchUpdate(content, path string, chunks []structuredPatchCh
 		if len(chunk.old) == 0 {
 			// A context anchor identifies the line immediately before a pure
 			// insertion. Only an explicit end-of-file hunk (or an unanchored
-			// insertion) belongs at the file end.
+			// insertion) belongs at the file end. A unified diff names the
+			// insertion point in its range instead; a zero-context hunk (as
+			// from `git diff -U0`) has nothing to verify the position against,
+			// so it is position-trusting by design — the same semantics git
+			// apply uses without fuzz. Hunks that carry context are verified.
 			start := lineIndex
-			if chunk.endOfFile || !chunk.hasContext {
+			if chunk.hasHint {
+				start = max(chunk.hint, lineIndex)
+			} else if chunk.endOfFile || !chunk.hasContext {
 				start = len(lines)
 			}
 			if start > len(lines) {
@@ -405,7 +498,13 @@ func applyStructuredPatchUpdate(content, path string, chunks []structuredPatchCh
 			lineIndex = start
 			continue
 		}
-		index, ambiguous := findStructuredPatchSequence(lines, chunk.old, lineIndex, chunk.endOfFile)
+		var index int
+		ambiguous := false
+		if chunk.hasHint && chunk.hint >= lineIndex && sequenceMatchesAt(lines, chunk.old, chunk.hint) {
+			index = chunk.hint
+		} else {
+			index, ambiguous = findStructuredPatchSequence(lines, chunk.old, lineIndex, chunk.endOfFile)
+		}
 		if ambiguous {
 			return "", fmt.Errorf("expected lines are ambiguous in %s; provide more surrounding context:\n%s", path, strings.Join(chunk.old, "\n"))
 		}
@@ -440,6 +539,64 @@ func applyStructuredPatchUpdate(content, path string, chunks []structuredPatchCh
 	return updated, nil
 }
 
+// verifyUnifiedDeletion checks, byte for byte, that the lines a unified
+// deletion removes are exactly the file's current content. A deletion is not
+// recoverable, so none of the whitespace tolerance used to locate update
+// hunks applies here; only the file's own line-ending style is normalised.
+// With no hunks (git's header-only form) the file must be empty.
+func verifyUnifiedDeletion(current, path string, operation structuredPatchOperation) error {
+	var removed []string
+	for _, chunk := range operation.chunks {
+		if len(chunk.new) > 0 {
+			return fmt.Errorf("deletion of %s must not add lines", path)
+		}
+		removed = append(removed, chunk.old...)
+	}
+	expected := strings.Join(removed, "\n")
+	if len(removed) > 0 && !operation.oldNoNewline {
+		expected += "\n"
+	}
+	actual := current
+	if structuredPatchLineEnding(current) == "\r\n" {
+		actual = strings.ReplaceAll(current, "\r\n", "\n")
+	}
+	if actual != expected {
+		if len(removed) == 0 {
+			return fmt.Errorf("deletion of %s expects an empty file but it has content; include the removed lines in the patch", path)
+		}
+		return fmt.Errorf("deletion of %s does not match its current content; the removed lines must equal the whole file", path)
+	}
+	return nil
+}
+
+// sequenceMatchesAt reports whether wanted appears verbatim at lines[start:].
+func sequenceMatchesAt(lines, wanted []string, start int) bool {
+	if start < 0 || start+len(wanted) > len(lines) {
+		return false
+	}
+	for offset, line := range wanted {
+		if lines[start+offset] != line {
+			return false
+		}
+	}
+	return true
+}
+
+// applyEOFNewline forces or strips a single trailing line ending when a
+// unified diff's end-of-file marker asked for it.
+func applyEOFNewline(content string, mode eofNewlineMode) string {
+	switch mode {
+	case eofNewlinePresent:
+		if content != "" && !strings.HasSuffix(content, "\n") {
+			return content + structuredPatchLineEnding(content)
+		}
+	case eofNewlineAbsent:
+		content = strings.TrimSuffix(content, "\n")
+		content = strings.TrimSuffix(content, "\r")
+	}
+	return content
+}
+
 func structuredPatchReplacement(chunk structuredPatchChunk, source []string, start int) ([]string, error) {
 	if len(chunk.newSourceOffsets) != len(chunk.new) {
 		return nil, fmt.Errorf("context mapping has %d entries for %d output lines", len(chunk.newSourceOffsets), len(chunk.new))
@@ -516,14 +673,19 @@ func findStructuredPatchSequence(lines, wanted []string, start int, endOfFile bo
 }
 
 func applyStructuredPatchChanges(root *os.Root, changes []structuredPatchChange, tracker *FileTracker) error {
-	mutated := false
+	// committed lists, in order, the paths whose change reached disk before a
+	// later change failed, so the caller (and the model) knows exactly which
+	// files now hold the patched content and which were never touched.
+	var committed []string
 	for _, change := range changes {
-		committed, err := applyStructuredPatchChange(root, change)
-		mutated = mutated || committed
+		done, err := applyStructuredPatchChange(root, change)
+		if done {
+			committed = append(committed, structuredPatchChangePaths(change)...)
+		}
 		if err != nil {
 			forgetStructuredPatchFiles(tracker, changes)
-			if mutated {
-				return fmt.Errorf("%w; structured patch was partially applied; re-read affected files before retrying", err)
+			if len(committed) > 0 {
+				return fmt.Errorf("%w; patch was partially applied — already committed: %s; the remaining files are unchanged; re-read the committed files before retrying", err, strings.Join(committed, ", "))
 			}
 			return err
 		}
@@ -531,6 +693,19 @@ func applyStructuredPatchChanges(root *os.Root, changes []structuredPatchChange,
 	return nil
 }
 
+// structuredPatchChangePaths names the workspace-relative paths a committed
+// change touched: the destination, plus the source of a move or copy.
+func structuredPatchChangePaths(change structuredPatchChange) []string {
+	if change.kind == structuredPatchDelete {
+		return []string{change.from.relative}
+	}
+	paths := []string{change.to.relative}
+	if change.from.absolute != change.to.absolute && change.from.relative != "" {
+		paths = append([]string{change.from.relative}, paths...)
+	}
+	return paths
+}
+
 func forgetStructuredPatchFiles(tracker *FileTracker, changes []structuredPatchChange) {
 	if tracker == nil {
 		return
@@ -543,14 +718,35 @@ func forgetStructuredPatchFiles(tracker *FileTracker, changes []structuredPatchC
 	}
 }
 
+// structuredPatchBeforeCommit, when set, runs before each change's pre-commit
+// recheck. Tests use it to alter the filesystem between planning and commit
+// deterministically; it is nil in production.
+var structuredPatchBeforeCommit func(change structuredPatchChange)
+
 func applyStructuredPatchChange(root *os.Root, change structuredPatchChange) (bool, error) {
+	if structuredPatchBeforeCommit != nil {
+		structuredPatchBeforeCommit(change)
+	}
+	// The planner validated the source against the bytes it read; re-read
+	// through the same root immediately before committing so a change made
+	// by another process in between is refused rather than overwritten or
+	// removed.
+	if change.kind != structuredPatchAdd {
+		current, err := root.ReadFile(change.from.relative)
+		if err != nil {
+			return false, fmt.Errorf("re-reading %s before commit: %w", change.from.relative, err)
+		}
+		if string(current) != change.before {
+			return false, fmt.Errorf("%s changed on disk between planning and commit; re-read it and retry", change.from.relative)
+		}
+	}
 	switch change.kind {
 	case structuredPatchDelete:
 		if err := root.Remove(change.from.relative); err != nil {
 			return false, fmt.Errorf("deleting %s: %w", change.from.relative, err)
 		}
 		return true, nil
-	case structuredPatchAdd:
+	case structuredPatchAdd, structuredPatchCopy:
 		return writeStructuredPatchFile(root, change.to, change.after, change.mode, true)
 	case structuredPatchUpdate:
 		moving := change.from.absolute != change.to.absolute
@@ -706,7 +902,7 @@ func recordStructuredPatchFile(tracker *FileTracker, absolute string, created, s
 	info, _ := os.Stat(absolute)
 	tracker.Record(absolute, content, info)
 	if seenWhole {
-		lines := lineCount(string(content))
+		lines := trackedLineTotal(string(content))
 		tracker.RecordSeenRange(absolute, 1, lines, lines)
 	}
 	if created {

internal/tools/tracked_line_total_test.go

@@ -0,0 +1,59 @@
+package tools
+
+import (
+	"context"
+	"fmt"
+	"path/filepath"
+	"testing"
+)
+
+func TestTrackedLineTotalMatchesReadFileStats(t *testing.T) {
+	root := t.TempDir()
+	for name, content := range map[string]string{"trailing": "a\nb\nc\n", "unterminated": "a\nb\nc", "single": "x\n", "empty": "", "crlf": "a\r\nb\r\n"} {
+		path := filepath.Join(root, name+".txt")
+		writeTestFile(t, path, content)
+		stats, err := scanReadFileStats(path)
+		if err != nil {
+			t.Fatal(err)
+		}
+		if got := trackedLineTotal(content); got != stats.lines {
+			t.Fatalf("%s: trackedLineTotal = %d, read_file reports %d", name, got, stats.lines)
+		}
+	}
+}
+
+// A whole-file read, an edit, then a partial re-read must keep the file "seen
+// whole": the writer and reader now agree on the line total, so the partial
+// read accumulates instead of resetting and a later edit far from the re-read
+// window is not refused.
+func TestEditThenPartialReadKeepsWholeFileObservation(t *testing.T) {
+	root := t.TempDir()
+	path := filepath.Join(root, "notes.txt")
+	content := ""
+	for i := 1; i <= 40; i++ {
+		content += fmt.Sprintf("line %02d\n", i)
+	}
+	writeTestFile(t, path, content)
+	tracker := NewFileTracker()
+	registry := NewRegistry()
+	registry.Register(NewScopedReadFileTool(root, nil))
+	registry.Register(NewScopedEditFileTool(root, nil))
+	opts := RunOptions{PermissionGranted: true, FileTracker: tracker}
+
+	if r := registry.RunWithOptions(context.Background(), "read_file", map[string]any{"path": "notes.txt"}, opts); r.Status != StatusOK {
+		t.Fatalf("read: %s", r.Output)
+	}
+	if r := registry.RunWithOptions(context.Background(), "edit_file", map[string]any{"path": "notes.txt", "old_string": "line 01\nline 02\n", "new_string": "line 01\nline two\n"}, opts); r.Status != StatusOK {
+		t.Fatalf("first edit: %s", r.Output)
+	}
+	if r := registry.RunWithOptions(context.Background(), "read_file", map[string]any{"path": "notes.txt", "limit": 5}, opts); r.Status != StatusOK {
+		t.Fatalf("partial read: %s", r.Output)
+	}
+	absolute, _ := filepath.EvalSymlinks(path)
+	if !tracker.SeenWhole(absolute) {
+		t.Fatal("partial re-read of an unchanged file must not discard whole-file knowledge")
+	}
+	if r := registry.RunWithOptions(context.Background(), "edit_file", map[string]any{"path": "notes.txt", "old_string": "line 39\nline 40\n", "new_string": "line 39\nline forty\n"}, opts); r.Status != StatusOK {
+		t.Fatalf("edit far from the re-read window must succeed: %s", r.Output)
+	}
+}

internal/tools/unified_patch.go

@@ -0,0 +1,393 @@
+package tools
+
+import (
+	"fmt"
+	"strings"
+)
+
+// parseUnifiedPatch converts a unified diff into the same operations a
+// structured patch produces, so both formats are applied by Zero itself
+// through an opened workspace root (descriptor-relative, no-follow writes)
+// instead of handing pathnames to git apply after validation.
+//
+// Supported: file modifications, creations (--- /dev/null) and deletions
+// (+++ /dev/null, verified against the content the hunks expect to remove),
+// multiple hunks per file, "\ No newline at end of file"
+// markers, a/ and b/ prefixes, git C-quoted paths, CRLF patches, and git's
+// "rename from/to" and "copy from/to" headers (with or without hunks). Headers
+// git emits around a hunk (diff --git, index, mode lines) are skipped; binary
+// patches are rejected.
+func parseUnifiedPatch(patch string) ([]structuredPatchOperation, error) {
+	normalized := strings.TrimPrefix(strings.ReplaceAll(patch, "\r\n", "\n"), "\ufeff")
+	lines := strings.Split(normalized, "\n")
+	// The element after a final "\n" is the line terminator, not an empty
+	// context line; counting it would let a truncated hunk look complete.
+	if len(lines) > 0 && lines[len(lines)-1] == "" {
+		lines = lines[:len(lines)-1]
+	}
+
+	var operations []structuredPatchOperation
+	var current *structuredPatchOperation
+	var chunk *structuredPatchChunk
+	var added []string // collected "+" lines for a file creation
+	oldPath, newPath := "", ""
+	pendingFrom, pendingKind := "", structuredPatchUpdate
+	// git's header-only forms: "deleted file mode" / "new file mode" after a
+	// "diff --git" line with no ---/+++ pair describe an empty file.
+	diffPath, headerOnly := "", byte(0) // headerOnly is 'd' (deleted) or 'n' (new)
+	oldRemaining, newRemaining := 0, 0
+	inHunk := false
+	lastSide := byte(0) // '+' or '-' for the most recent content line
+
+	finish := func() error {
+		if current == nil {
+			return nil
+		}
+		switch current.kind {
+		case structuredPatchAdd:
+			if len(added) > 0 {
+				current.contents = strings.Join(added, "\n")
+				if current.eofNewline != eofNewlineAbsent {
+					current.contents += "\n"
+				}
+			}
+		case structuredPatchUpdate, structuredPatchCopy:
+			if !allStructuredPatchChunksHaveContent(current.chunks) {
+				return fmt.Errorf("unified diff for %s has an empty hunk", current.path)
+			}
+			if len(current.chunks) == 0 && current.movePath == "" {
+				return fmt.Errorf("unified diff for %s has no hunk lines", current.path)
+			}
+		case structuredPatchDelete:
+			if len(current.chunks) == 0 || !allStructuredPatchChunksHaveContent(current.chunks) {
+				return fmt.Errorf("unified deletion of %s must include the hunk with the content being removed", current.path)
+			}
+		}
+		operations = append(operations, *current)
+		current, chunk, added = nil, nil, nil
+		return nil
+	}
+	flushHeaderOnly := func(line int) error {
+		if headerOnly == 0 {
+			return nil
+		}
+		if diffPath == "" {
+			return fmt.Errorf("invalid unified diff at line %d: file mode header without a diff --git path", line)
+		}
+		if err := finish(); err != nil {
+			return err
+		}
+		switch headerOnly {
+		case 'd':
+			operations = append(operations, structuredPatchOperation{kind: structuredPatchDelete, path: diffPath, line: line, verifyDelete: true})
+		case 'n':
+			operations = append(operations, structuredPatchOperation{kind: structuredPatchAdd, path: diffPath, line: line})
+		}
+		headerOnly, diffPath = 0, ""
+		return nil
+	}
+	startFile := func(line int) error {
+		// A ---/+++ pair means the file has hunks; it is not header-only.
+		headerOnly, diffPath = 0, ""
+		if oldPath == "" || newPath == "" {
+			return fmt.Errorf("invalid unified diff at line %d: hunk before a ---/+++ header pair", line)
+		}
+		// A ---/+++ pair after a rename/copy header names the same files; keep
+		// accumulating that operation's hunks instead of starting a new one.
+		if current != nil && current.movePath != "" && current.path == oldPath && (current.movePath == newPath || oldPath == newPath) {
+			return nil
+		}
+		if err := finish(); err != nil {
+			return err
+		}
+		op := structuredPatchOperation{line: line}
+		switch {
+		case oldPath == "/dev/null" && newPath == "/dev/null":
+			return fmt.Errorf("invalid unified diff at line %d: both sides are /dev/null", line)
+		case oldPath == "/dev/null":
+			op.kind, op.path = structuredPatchAdd, newPath
+		case newPath == "/dev/null":
+			// A unified deletion states the content it expects to remove; keep
+			// its hunks so the planner verifies them before deleting.
+			op.kind, op.path, op.verifyDelete = structuredPatchDelete, oldPath, true
+		default:
+			op.kind, op.path = structuredPatchUpdate, oldPath
+			if newPath != oldPath {
+				op.movePath = newPath
+			}
+		}
+		current = &op
+		return nil
+	}
+
+	for index, raw := range lines {
+		lineNumber := index + 1
+		if inHunk && (oldRemaining > 0 || newRemaining > 0) {
+			// A "--- " line followed by "+++ " and then a "@@" hunk header is
+			// the next file's header pair, not a removed "-- x" line followed by
+			// an added "++ y" line: an over-declared count would otherwise
+			// swallow both and the hunk would later fail against the wrong
+			// file. The "@@" requirement keeps a genuine adjacent pair intact.
+			if strings.HasPrefix(raw, "--- ") && index+2 < len(lines) && strings.HasPrefix(lines[index+1], "+++ ") && strings.HasPrefix(lines[index+2], "@@") {
+				return nil, fmt.Errorf("invalid unified diff at line %d: hunk ended before its declared line counts", lineNumber)
+			}
+			switch {
+			case strings.HasPrefix(raw, "\\"):
+				// "\ No newline at end of file" qualifies the previous line's side.
+				if current != nil && lastSide == '+' {
+					current.eofNewline = eofNewlineAbsent
+				} else if current != nil && lastSide == '-' {
+					current.oldNoNewline = true
+					if current.eofNewline == eofNewlineKeep {
+						current.eofNewline = eofNewlinePresent
+					}
+				}
+				continue
+			case strings.HasPrefix(raw, "-"):
+				oldRemaining--
+				lastSide = '-'
+				if chunk != nil {
+					chunk.old = append(chunk.old, raw[1:])
+				}
+			case strings.HasPrefix(raw, "+"):
+				newRemaining--
+				lastSide = '+'
+				if current != nil && current.kind == structuredPatchAdd {
+					added = append(added, raw[1:])
+				} else if chunk != nil {
+					chunk.new = append(chunk.new, raw[1:])
+					chunk.newSourceOffsets = append(chunk.newSourceOffsets, -1)
+				}
+			default:
+				content := raw
+				if strings.HasPrefix(raw, " ") {
+					content = raw[1:]
+				} else if raw != "" {
+					return nil, fmt.Errorf("invalid unified diff at line %d: hunk lines must start with ' ', '+', '-' or '\\'", lineNumber)
+				}
+				oldRemaining--
+				newRemaining--
+				lastSide = ' '
+				if chunk != nil {
+					offset := len(chunk.old)
+					chunk.old = append(chunk.old, content)
+					chunk.new = append(chunk.new, content)
+					chunk.newSourceOffsets = append(chunk.newSourceOffsets, offset)
+				}
+			}
+			continue
+		}
+		inHunk = false
+		trimmed := strings.TrimSpace(raw)
+		if oldRemaining > 0 || newRemaining > 0 {
+			// The hunk ended before its declared counts were consumed. Report
+			// it here rather than absorbing the next file's ---/+++ headers as
+			// "-"/"+" content and failing later against the wrong file.
+			return nil, fmt.Errorf("invalid unified diff at line %d: hunk ended before its declared line counts", lineNumber)
+		}
+		switch {
+		case trimmed == "":
+			continue
+		case strings.HasPrefix(raw, "\\"):
+			// "\ No newline at end of file" directly after a hunk's last line.
+			if current != nil && lastSide == '+' {
+				current.eofNewline = eofNewlineAbsent
+			} else if current != nil && lastSide == '-' {
+				current.oldNoNewline = true
+				if current.eofNewline == eofNewlineKeep {
+					current.eofNewline = eofNewlinePresent
+				}
+			}
+			continue
+		case strings.HasPrefix(raw, "diff --git "):
+			if err := flushHeaderOnly(lineNumber); err != nil {
+				return nil, err
+			}
+			diffPath = diffGitNewPath(raw)
+			continue
+		case strings.HasPrefix(raw, "deleted file mode "):
+			headerOnly = 'd'
+			continue
+		case strings.HasPrefix(raw, "new file mode "):
+			headerOnly = 'n'
+			continue
+		case strings.HasPrefix(raw, "index "), strings.HasPrefix(raw, "old mode "), strings.HasPrefix(raw, "new mode "):
+			continue
+		case strings.HasPrefix(raw, "similarity index "), strings.HasPrefix(raw, "dissimilarity index "):
+			continue
+		case strings.HasPrefix(raw, "rename from "), strings.HasPrefix(raw, "copy from "):
+			pendingFrom = strings.TrimSpace(unquoteGitPath(strings.TrimPrefix(strings.TrimPrefix(raw, "rename from "), "copy from ")))
+			pendingKind = structuredPatchUpdate
+			if strings.HasPrefix(raw, "copy from ") {
+				pendingKind = structuredPatchCopy
+			}
+			if pendingFrom == "" {
+				return nil, fmt.Errorf("invalid unified diff at line %d: missing source path", lineNumber)
+			}
+		case strings.HasPrefix(raw, "rename to "), strings.HasPrefix(raw, "copy to "):
+			to := strings.TrimSpace(unquoteGitPath(strings.TrimPrefix(strings.TrimPrefix(raw, "rename to "), "copy to ")))
+			if pendingFrom == "" || to == "" {
+				return nil, fmt.Errorf("invalid unified diff at line %d: rename/copy destination without a source", lineNumber)
+			}
+			if err := finish(); err != nil {
+				return nil, err
+			}
+			current = &structuredPatchOperation{kind: pendingKind, path: pendingFrom, movePath: to, line: lineNumber}
+			oldPath, newPath, pendingFrom = pendingFrom, to, ""
+		case strings.HasPrefix(raw, "Binary files "), strings.HasPrefix(raw, "GIT binary patch"):
+			return nil, fmt.Errorf("invalid unified diff at line %d: binary patches are not supported", lineNumber)
+		case strings.HasPrefix(raw, "--- "):
+			oldPath = stripPatchPrefix(patchFileHeaderPath(raw))
+			newPath = ""
+			if oldPath == "" {
+				return nil, fmt.Errorf("invalid unified diff at line %d: missing path in --- header", lineNumber)
+			}
+		case strings.HasPrefix(raw, "+++ "):
+			newPath = stripPatchPrefix(patchFileHeaderPath(raw))
+			if newPath == "" {
+				return nil, fmt.Errorf("invalid unified diff at line %d: missing path in +++ header", lineNumber)
+			}
+			if err := startFile(lineNumber); err != nil {
+				return nil, err
+			}
+		case strings.HasPrefix(raw, "@@"):
+			if current == nil {
+				return nil, fmt.Errorf("invalid unified diff at line %d: hunk before a ---/+++ header pair", lineNumber)
+			}
+			oldStart, oldCount, newCount, ok := parseHunkRange(raw)
+			if !ok {
+				return nil, fmt.Errorf("invalid unified diff at line %d: malformed hunk header", lineNumber)
+			}
+			// "\ No newline at end of file" describes the end of the file, so it
+			// may only follow a file's final hunk; a marker before another hunk
+			// would otherwise leak into that later hunk's result.
+			if current.eofNewline != eofNewlineKeep {
+				return nil, fmt.Errorf("invalid unified diff at line %d: \"\\ No newline at end of file\" must follow the last hunk of a file", lineNumber)
+			}
+			oldRemaining, newRemaining = oldCount, newCount
+			inHunk = oldRemaining > 0 || newRemaining > 0
+			lastSide = 0
+			if current.kind != structuredPatchAdd {
+				next := structuredPatchChunk{hasHint: true, hint: oldStart - 1}
+				if oldCount == 0 {
+					// A pure insertion's range names the line after which the
+					// new lines go, so the insertion index is oldStart itself.
+					next.hint = oldStart
+				}
+				if next.hint < 0 {
+					next.hint = 0
+				}
+				current.chunks = append(current.chunks, next)
+				chunk = &current.chunks[len(current.chunks)-1]
+			}
+		default:
+			return nil, fmt.Errorf("invalid unified diff at line %d: unexpected %q", lineNumber, trimmed)
+		}
+	}
+	// Strict at end of input on purpose: a hunk cut short (typically a model
+	// response that stopped mid-patch) would otherwise apply as a partial
+	// change — removals without their replacements — which is worse than a
+	// clear error and a retry. Miscounted ranges with complete content are
+	// still tolerated at every other boundary.
+	if inHunk && (oldRemaining > 0 || newRemaining > 0) {
+		return nil, fmt.Errorf("invalid unified diff at line %d: hunk ended before its declared line counts", len(lines))
+	}
+	if err := flushHeaderOnly(len(lines)); err != nil {
+		return nil, err
+	}
+	if err := finish(); err != nil {
+		return nil, err
+	}
+	if len(operations) == 0 {
+		return nil, fmt.Errorf("unified diff contains no file changes")
+	}
+	return operations, nil
+}
+
+// diffGitNewPath returns the post-image path named by a "diff --git a/X b/Y"
+// line, handling git's C-quoted form; "" when it cannot be determined.
+func diffGitNewPath(line string) string {
+	rest := strings.TrimSpace(strings.TrimPrefix(line, "diff --git "))
+	if strings.HasPrefix(rest, "\"") {
+		// Two quoted tokens: skip the first, unquote the second.
+		end := strings.Index(rest[1:], "\"")
+		for end > 0 && rest[end] == '\\' {
+			next := strings.Index(rest[end+2:], "\"")
+			if next < 0 {
+				return ""
+			}
+			end += next + 2
+		}
+		if end < 0 || end+2 > len(rest) {
+			return ""
+		}
+		rest = strings.TrimSpace(rest[end+2:])
+		return stripPatchPrefix(unquoteGitPath(rest))
+	}
+	fields := strings.Fields(rest)
+	if len(fields) < 2 {
+		return ""
+	}
+	last := fields[len(fields)-1]
+	if strings.HasPrefix(last, "\"") {
+		return stripPatchPrefix(unquoteGitPath(last))
+	}
+	return stripPatchPrefix(last)
+}
+
+// parseHunkRange reads "@@ -a[,b] +c[,d] @@" and returns a, b and d; a missing
+// count means 1 per unified-diff convention.
+func parseHunkRange(line string) (oldStart, oldCount, newCount int, ok bool) {
+	_, rest, found := strings.Cut(line, "@@")
+	if !found {
+		return 0, 0, 0, false
+	}
+	rangeSection := rest
+	if before, _, found := strings.Cut(rest, "@@"); found {
+		rangeSection = before
+	}
+	fields := strings.Fields(rangeSection)
+	if len(fields) != 2 || !strings.HasPrefix(fields[0], "-") || !strings.HasPrefix(fields[1], "+") {
+		return 0, 0, 0, false
+	}
+	parse := func(spec string) (int, int, bool) {
+		startText, countText, hasCount := strings.Cut(spec, ",")
+		start, err := parseNonNegativeInt(startText)
+		if err != nil {
+			return 0, 0, false
+		}
+		count := 1
+		if hasCount {
+			if count, err = parseNonNegativeInt(countText); err != nil {
+				return 0, 0, false
+			}
+		}
+		return start, count, true
+	}
+	oldStart, oldCount, ok = parse(fields[0][1:])
+	if !ok {
+		return 0, 0, 0, false
+	}
+	_, newCount, ok = parse(fields[1][1:])
+	if !ok {
+		return 0, 0, 0, false
+	}
+	return oldStart, oldCount, newCount, true
+}
+
+func parseNonNegativeInt(text string) (int, error) {
+	if text == "" {
+		return 0, fmt.Errorf("empty number")
+	}
+	value := 0
+	for _, r := range text {
+		if r < '0' || r > '9' {
+			return 0, fmt.Errorf("not a number: %q", text)
+		}
+		value = value*10 + int(r-'0')
+		if value > 1<<30 {
+			return 0, fmt.Errorf("number too large: %q", text)
+		}
+	}
+	return value, nil
+}

internal/tools/write_file.go

@@ -120,7 +120,7 @@ func (tool writeFileTool) RunWithOptions(ctx context.Context, args map[string]an
 	newInfo, _ := os.Stat(absolutePath)
 	options.FileTracker.Record(absolutePath, []byte(content), newInfo)
 	if content == modelKnownContent {
-		options.FileTracker.RecordSeenRange(absolutePath, 1, lineCount(content), lineCount(content))
+		options.FileTracker.RecordSeenRange(absolutePath, 1, trackedLineTotal(content), trackedLineTotal(content))
 	}
 	if !existed {
 		options.FileTracker.RecordCreated(absolutePath)

internal/tools/write_tools_test.go

@@ -866,7 +866,9 @@ func TestStructuredPatchFailedDeleteDoesNotRecreateMissingFile(t *testing.T) {
 	}
 }
 
-func TestStructuredPatchMoveFailureLeavesPublishedDestination(t *testing.T) {
+// A move whose source vanishes after planning is refused by the pre-commit
+// recheck before the destination is published, so nothing is left half-done.
+func TestStructuredPatchMoveWithMissingSourceIsRefusedBeforePublishing(t *testing.T) {
 	root := t.TempDir()
 	workspace, err := os.OpenRoot(root)
 	if err != nil {
@@ -875,22 +877,35 @@ func TestStructuredPatchMoveFailureLeavesPublishedDestination(t *testing.T) {
 	defer workspace.Close()
 	sourcePath := filepath.Join(root, "source.txt")
 	destinationPath := filepath.Join(root, "destination.txt")
+	writeTestFile(t, sourcePath, "removed source\n")
 	change := structuredPatchChange{
 		kind:   structuredPatchUpdate,
 		from:   structuredPatchTarget{absolute: sourcePath, relative: "source.txt"},
 		to:     structuredPatchTarget{absolute: destinationPath, relative: "destination.txt"},
 		before: "removed source\n", after: "moved content\n", mode: 0o644,
 	}
+	// The source exists at planning time and disappears just before commit.
+	removed := false
+	structuredPatchBeforeCommit = func(structuredPatchChange) {
+		if err := os.Remove(sourcePath); err != nil {
+			t.Fatal(err)
+		}
+		removed = true
+	}
+	defer func() { structuredPatchBeforeCommit = nil }()
 
 	err = applyStructuredPatchChanges(workspace, []structuredPatchChange{change}, nil)
-	if err == nil || !strings.Contains(err.Error(), "partially applied") {
-		t.Fatalf("move with a missing source = %v, want partial-application error", err)
+	if !removed {
+		t.Fatal("pre-commit hook did not run")
+	}
+	if err == nil || !strings.Contains(err.Error(), "before commit") || strings.Contains(err.Error(), "partially applied") {
+		t.Fatalf("move with a missing source = %v, want a pre-commit refusal with nothing applied", err)
 	}
 	if _, statErr := os.Stat(sourcePath); !os.IsNotExist(statErr) {
 		t.Fatalf("failed move recreated a missing source: %v", statErr)
 	}
-	if got := mustReadTestFile(t, destinationPath); got != "moved content\n" {
-		t.Fatalf("published move destination = %q", got)
+	if _, statErr := os.Stat(destinationPath); !os.IsNotExist(statErr) {
+		t.Fatalf("refused move must not publish the destination: %v", statErr)
 	}
 }
 

internal/tui/model_test.go

@@ -2439,7 +2439,7 @@ func TestAssistantNarrationBeforeToolCardGetsBlankSeparator(t *testing.T) {
 	m.transcript = append(m.transcript,
 		transcriptRow{kind: rowUser, text: "run it"},
 		transcriptRow{kind: rowAssistant, text: "I'll inspect the existing file, then run it."},
-		transcriptRow{kind: rowToolResult, id: "t1", tool: "read_file", status: tools.StatusOK, detail: "File: time_test.py\n\n  1 | print('x')"},
+		transcriptRow{kind: rowToolResult, id: "t1", tool: "read_file", status: tools.StatusOK, detail: "File: time_test.py\n\n1→print('x')"},
 	)
 	items := m.transcriptBodyItems(m.chatColumnWidth(), "", false)
 	toolIdx := -1

internal/tui/rendering_lime_test.go

@@ -1075,8 +1075,8 @@ func TestEditedDiffCardHandlesBareBlankHunkContext(t *testing.T) {
 
 func TestReadCardBodyShowsExploredSummary(t *testing.T) {
 	m := limeTestModel()
-	// Mirrors the real read_file output shape: "<right-aligned N> | <text>".
-	detail := "File: internal/agent/loop.go\n\n  12 | func Run() {\n  13 | }\n"
+	// Mirrors the real read_file output shape: "N→<text>".
+	detail := "File: internal/agent/loop.go\n\n12→func Run() {\n13→}\n"
 	row := transcriptRow{kind: rowToolResult, id: "call_1", tool: "read_file", status: tools.StatusOK, detail: detail}
 	rc := buildRowContext([]transcriptRow{{kind: rowToolCall, id: "call_1", tool: "read_file", detail: "internal/agent/loop.go"}})
 	got := plainRender(t, m.renderRow(row, 80, rc))
@@ -1097,7 +1097,7 @@ func TestReadCardBodyShowsExploredSummary(t *testing.T) {
 
 	row.expanded = true
 	expanded := plainRender(t, m.renderRow(row, 80, rc))
-	for _, want := range []string{"Explored", "└ Read", "internal/agent/loop.go", "func Run()", "13 |"} {
+	for _, want := range []string{"Explored", "└ Read", "internal/agent/loop.go", "func Run()", "13→"} {
 		if !strings.Contains(expanded, want) {
 			t.Fatalf("expanded read card = %q, missing %q", expanded, want)
 		}

internal/tui/tool_render_registry_test.go

@@ -41,7 +41,7 @@ func TestDefaultToolBodyRegistrySelectsCoreRenderers(t *testing.T) {
 		{
 			name:   "read_file",
 			hint:   "README.md",
-			detail: "File: README.md\n\n  7 | # Zero",
+			detail: "File: README.md\n\n7→# Zero",
 			want:   []string{"Read", "README.md"},
 		},
 		{