fix(packages): show the guidance file an install left as it is, and verify an install that only skipped

rig package install now prints the install's notes under "Left as it is:",
and bootstrap adds them to its warnings, so a guidance file whose block
was left untouched is named with its reason instead of vanishing from the
"Installed:" list.

An install whose only entries were skipped on purpose (each named in its
notes) now verifies as entries_skipped rather than failing as an empty
journal. The route answers 201 with the note, and bootstrap still imports
the rig beside the package's other installs. An empty journal with no
named skip still fails verification. A 500 verification failure also
returns the notes.

docs/reference/agent-startup-guide.md

@@ -405,6 +405,11 @@ Each startup file and action specifies when it applies:
 - a launch replaces it, as launches always did, and names it (`guidance_block_refreshed_unrecorded`);
 - an exact resume or a handover leaves it, and names it as possibly stale (`guidance_block_may_be_stale`).
 
+**A file keeps one copy of each block.**
+- **Touched markers:** a marker an editor or formatter rewrapped, with spaces or line breaks inside the comment, still reads as its block, and the next write puts it back in OpenRig's form.
+- **Collected copies:** they're reduced to the first. Beside a copy you edited, OpenRig's own unedited copies and exact repeats are removed, and every different edited copy stays (`guidance_block_copies_removed`).
+- **A marker that lost its pair:** OpenRig can't tell where that block starts or ends, so it adds no copy beside it and names it (`guidance_block_markers_damaged`). Put back the missing marker or remove the partial block, and OpenRig's next write keeps one block. `rig package install` leaves such a file as it is, names it in its result (`notes`), and installs the rest. A marker without its pair beside a complete block is named too (`guidance_block_marker_unpaired`), and the block is written.
+
 An exact resume doesn't type anything into the resumed conversation. So there, the restore result names the block (`guidanceNotes`), but the seat isn't told.
 
 Use this to avoid re-sending context that a fresh conversation doesn't need twice. For example, a one-time project briefing might only apply on `fresh_start`, while identity grounding should apply on both, so a seat that comes back fresh gets it again.

packages/cli/src/commands/package.ts

@@ -137,6 +137,7 @@ export function packageCommand(depsOverride?: StatusDeps): Command {
         conflicts?: Array<{ existingPath: string; reason: string }>;
         verification?: { passed: boolean };
         policyRejected?: Array<{ entry: { exportType: string; exportName: string }; reason: string }>;
+        notes?: string[];
         error?: string;
         errors?: string[];
         code?: string;
@@ -204,6 +205,11 @@ export function packageCommand(depsOverride?: StatusDeps): Command {
           console.log(`  ${r.entry.exportType.padEnd(12)} ${r.entry.exportName.padEnd(20)} ${r.reason}`);
         }
       }
+
+      if (res.data.notes && res.data.notes.length > 0) {
+        console.log("Left as it is:");
+        for (const note of res.data.notes) console.log(`  ${note}`);
+      }
     });
 
   // rig package rollback <installId>

packages/cli/test/package.test.ts

@@ -207,6 +207,20 @@ function createMockDaemon() {
         }));
         return;
       }
+      if (sourceRef.includes("skipped")) {
+        res.writeHead(201, { "Content-Type": "application/json" });
+        res.end(JSON.stringify({
+          installId: "inst-skip-1",
+          packageId: "pkg-1",
+          packageName: "guidance-pkg",
+          applied: [],
+          deferred: [],
+          conflicts: [],
+          verification: { passed: true },
+          notes: ["guidance_block_markers_damaged: /repo/CLAUDE.md: guidance-pkg has a BEGIN or END marker without its pair"],
+        }));
+        return;
+      }
       if (sourceRef.includes("merge")) {
         res.writeHead(201, { "Content-Type": "application/json" });
         res.end(JSON.stringify({
@@ -383,6 +397,14 @@ describe("rig package", () => {
     expect(output).toContain("inst-merge-1");
   });
 
+  it("install with a guidance file left as it is: names the file and the reason, exit 0", async () => {
+    const { logs, exitCode } = await captureLogs(() => makeProgram().parseAsync(["node", "rig", "package", "install", "/skipped/path", "--target", "/repo", "--allow-merge"]));
+    const output = logs.join("\n");
+    expect(output).toContain("Left as it is:");
+    expect(output).toContain("  guidance_block_markers_damaged: /repo/CLAUDE.md: guidance-pkg has a BEGIN or END marker without its pair");
+    expect(exitCode).toBeUndefined();
+  });
+
   // Test 8: install conflicts (409) → exitCode 1
   it("install conflicts: prints conflicts, exitCode 1", async () => {
     const { logs, exitCode } = await captureLogs(() => makeProgram().parseAsync(["node", "rig", "package", "install", "/conflict/path", "--target", "/repo"]));

packages/daemon/src/domain/bootstrap-orchestrator.ts

@@ -643,6 +643,9 @@ export class BootstrapOrchestrator {
         if (!outcome.ok) {
           errors.push(`Package install failed for '${ref}' (${runtime}): ${outcome.message}`);
           packageInstallFailed = true;
+        } else {
+          // A file the install left as it is, and why: the rest installed, and the rig still imports.
+          for (const note of outcome.notes ?? []) warnings.push(`Package '${ref}' (${runtime}): ${note}`);
         }
       }
     }

packages/daemon/src/domain/install-engine.ts

@@ -4,6 +4,7 @@ import type { InstallPlanEntry } from "./install-planner.js";
 import type { PolicyResult } from "./install-policy.js";
 import type { RefinedInstallPlan } from "./conflict-detector.js";
 import { InstallRepository, type JournalEntry } from "./install-repository.js";
+import { damagedManagedBlockNote, findManagedBlocks, managedBlockBodyMatches, mergeManagedBlockText } from "./managed-blocks.js";
 
 export interface EngineFsOps {
   readFile: (filePath: string) => string;
@@ -19,6 +20,8 @@ export interface InstallResult {
   applied: JournalEntry[];
   deferred: InstallPlanEntry[];
   conflicts: InstallPlanEntry[];
+  /** Entries left as they were, each with the reason: a guidance file whose block has a marker without its pair. */
+  notes: string[];
 }
 
 export interface RollbackResult {
@@ -52,10 +55,19 @@ export class InstallEngine {
   ): InstallResult {
     const install = this.installRepo.createInstall(packageId, targetRoot, "project_shared", bootstrapId);
     const applied: JournalEntry[] = [];
+    const notes: string[] = [];
     const backupRoot = path.join(targetRoot, ".rigged-backups", install.id);
 
     try {
       for (const entry of policyResult.approved) {
+        // A guidance block with a marker that lost its pair can't be replaced, and another copy beside it is the
+        // duplicate to avoid: that file is left as it is and named, and the rest of the install goes on.
+        const unreadable = entry.exportType === "guidance" ? this.unreadableGuidanceBlock(entry, plan.packageName) : null;
+        if (unreadable) {
+          notes.push(unreadable);
+          continue;
+        }
+
         // Ensure target directory
         this.fs.mkdirp(path.dirname(entry.targetPath));
 
@@ -121,6 +133,7 @@ export class InstallEngine {
       applied,
       deferred: plan.deferred,
       conflicts: plan.conflicts,
+      notes,
     };
   }
 
@@ -170,6 +183,14 @@ export class InstallEngine {
     return { restored, deleted };
   }
 
+  /** The note for a guidance entry whose target holds a marker of the package's block without its pair, and no complete
+   *  copy, or null. */
+  private unreadableGuidanceBlock(entry: InstallPlanEntry, packageName: string): string | null {
+    if (!entry.sourcePath || !this.fs.exists(entry.targetPath)) return null;
+    const found = findManagedBlocks(this.fs.readFile(entry.targetPath), packageName);
+    return found.blocks.length === 0 && found.unpaired > 0 ? damagedManagedBlockNote(entry.targetPath, packageName) : null;
+  }
+
   private applyGuidanceMerge(entry: InstallPlanEntry, packageName: string): void {
     if (!entry.sourcePath) return;
 
@@ -178,34 +199,17 @@ export class InstallEngine {
 
     if (this.fs.exists(entry.targetPath)) {
       const existing = this.fs.readFile(entry.targetPath);
-      const startMarker = BLOCK_START(packageName);
-      const endMarker = BLOCK_END(packageName);
-      const legacyStart = `<!-- BEGIN RIGGED MANAGED BLOCK: ${packageName} -->`;
-      const legacyEnd = `<!-- END RIGGED MANAGED BLOCK: ${packageName} -->`;
-      // Prefer the OpenRig form; fall back to legacy markers from
-      // prior installs so re-applying a guidance package over a
-      // pre-rename file replaces the old block instead of appending a
-      // duplicate.
-      let startIdx = existing.indexOf(startMarker);
-      let endIdx = existing.indexOf(endMarker, startIdx + startMarker.length);
-      let matchedEndLength = endMarker.length;
-      if (startIdx === -1 || endIdx === -1) {
-        const legacyStartIdx = existing.indexOf(legacyStart);
-        const legacyEndIdx = existing.indexOf(legacyEnd, legacyStartIdx + legacyStart.length);
-        if (legacyStartIdx !== -1 && legacyEndIdx !== -1) {
-          startIdx = legacyStartIdx;
-          endIdx = legacyEndIdx;
-          matchedEndLength = legacyEnd.length;
-        }
-      }
-
-      if (startIdx !== -1 && endIdx !== -1) {
-        // Update existing block (rewrites legacy markers to OpenRig form).
-        const updated = existing.slice(0, startIdx) + block + existing.slice(endIdx + matchedEndLength);
-        this.fs.writeFile(entry.targetPath, updated);
-      } else {
+      const found = findManagedBlocks(existing, packageName);
+      if (found.blocks.length === 0) {
         // Insert new block at end
         this.fs.writeFile(entry.targetPath, existing + "\n\n" + block + "\n");
+      } else {
+        // Update the first copy in place, in the OpenRig form (legacy markers too). A later copy goes when it repeats the
+        // first copy's text or the package's; a copy with other text, which someone wrote, stays.
+        const first = found.blocks[0]!.body;
+        const updated = mergeManagedBlockText(existing, packageName, block, [],
+          (body) => !managedBlockBodyMatches(body, first) && !managedBlockBodyMatches(body, content));
+        if (updated !== null) this.fs.writeFile(entry.targetPath, updated);
       }
     } else {
       // New file

packages/daemon/src/domain/install-verifier.ts

@@ -45,7 +45,9 @@ export class InstallVerifier {
     this.fs = fs;
   }
 
-  verify(installId: string): VerificationResult {
+  /** `skipped`: entries the install deliberately left as they were (its result's notes), so an install whose every entry was
+   *  skipped verifies as that, not as an empty journal. */
+  verify(installId: string, opts: { skipped?: number } = {}): VerificationResult {
     const install = this.installRepo.getInstall(installId);
     if (!install) {
       return {
@@ -76,6 +78,16 @@ export class InstallVerifier {
     const journal = this.installRepo.getJournalEntries(installId);
     const applyEntries = journal.filter((e) => e.action !== "rollback");
 
+    // Every entry left as it was on purpose, each named in the install's notes: nothing to check, and nothing missing.
+    if (applyEntries.length === 0 && (opts.skipped ?? 0) > 0) {
+      return {
+        passed: true,
+        installId,
+        entries: [],
+        statusCheck: { ...statusCheck, name: "entries_skipped", passed: true, expected: "applied entries, or skips named in notes", actual: `0 applied, ${opts.skipped} skipped` },
+      };
+    }
+
     // Empty journal for applied install is a verification failure
     if (applyEntries.length === 0) {
       return {

packages/daemon/src/domain/managed-block-records.ts

@@ -2,7 +2,8 @@ import { createHash } from "node:crypto";
 import fs from "node:fs";
 import nodePath from "node:path";
 import type Database from "better-sqlite3";
-import { frameManagedBlockBody, managedBlockStanding, mergeManagedBlock, type ManagedBlockMergeFsOps, type ManagedBlockStanding } from "./managed-blocks.js";
+import { damagedManagedBlockNote, frameManagedBlockBody, managedBlockBodyMatches, managedBlockStanding, mergeManagedBlock, pruneManagedBlockCopies,
+  withCanonicalMarkers, type ManagedBlockMergeFsOps, type ManagedBlockStanding } from "./managed-blocks.js";
 
 /** #2456: OpenRig's record of what it last wrote in each managed guidance block, so a later start, exact resume, handover
  *  or runtime switch can tell a block it wrote (refreshed when its source changes) from a block a person edited (kept). */
@@ -92,6 +93,8 @@ export function decideManagedBlock(content: string, blockId: string, source: str
   const standing = managedBlockStanding(content, blockId, source, recorded, managedBlockBodyHash);
   const named = opts.sourcePath ?? "its source";
   if (standing === "absent") return { standing, write: !opts.onlyIfPresent };
+  // A marker without its pair: writing would add a second copy beside the block that can't be read, at every start.
+  if (standing === "damaged") return { standing, write: false, note: damagedManagedBlockNote(targetPath, blockId) };
   if (unreadable && standing === "unrecorded") {
     return { standing: "unknown", write: false,
       note: `guidance_block_record_unreadable: ${targetPath}: ${blockId} wasn't refreshed from ${named} because OpenRig couldn't read its write record` };
@@ -103,10 +106,36 @@ export function decideManagedBlock(content: string, blockId: string, source: str
   return { standing, write: true };
 }
 
+/** A block that isn't rewritten (current, edited or unrecorded) can still carry extra copies, or markers an editor
+ *  rewrapped: take out the copies that repeat a kept one, and OpenRig's own (its source's text, or what it last wrote)
+ *  beside an edited one, so the file keeps one copy of each distinct text, and put the markers in OpenRig's form. Nothing
+ *  a person wrote is removed. Best effort: a file that can't be read or written is named in `notes` and left as it is,
+ *  and the block's own decision stands. Returns whether the file changed. */
+export function pruneKeptManagedBlock(files: ManagedBlockMergeFsOps, targetPath: string, blockId: string, source: string,
+  records: ManagedBlockRecords | undefined, notes?: string[]): boolean {
+  let recorded: string | undefined;
+  try { recorded = records?.get(targetPath, blockId); } catch { /* unreadable: only the source's text counts as OpenRig's */ }
+  try {
+    const existing = files.exists(targetPath) ? files.readFile(targetPath) : "";
+    const pruned = pruneManagedBlockCopies(existing, blockId,
+      (body) => managedBlockBodyMatches(body, source) || (recorded !== undefined && managedBlockBodyHash(body) === recorded));
+    const tidy = withCanonicalMarkers(pruned ?? existing, blockId);
+    if (tidy === existing) return false;
+    files.writeFile(targetPath, tidy);
+    if (pruned !== null) {
+      notes?.push(`guidance_block_copies_removed: ${targetPath}: ${blockId} had repeated copies; the repeats were removed and every edited copy was kept`);
+    }
+    return true;
+  } catch (err) {
+    notes?.push(`guidance_block_copies_not_removed: ${targetPath}: ${blockId}'s repeated copies or markers couldn't be tidied (${(err as Error).message}); the file was left as it is`);
+    return false;
+  }
+}
+
 /** #2456: the one write of a managed guidance block that every adapter's guidance merge goes through. Without `records` it's
- *  the plain merge, as before. With them, `decideManagedBlock` decides; a kept block is named in `warnings` and nothing is
- *  written. A written block is recorded at once, so a later failure in the same start can't lose its record. Returns
- *  whether the block was written. */
+ *  the plain merge, as before. With them, `decideManagedBlock` decides; a kept block is named in `warnings`, and only its
+ *  repeated copies are taken out (`pruneKeptManagedBlock`). A written block is recorded at once, so a later failure in the
+ *  same start can't lose its record. Returns whether the block was written. */
 export function writeManagedGuidanceBlock(files: ManagedBlockMergeFsOps, targetPath: string, blockId: string, content: string, opts: {
   records?: ManagedBlockRecords; unrecorded?: "keep" | "refresh"; onlyIfPresent?: boolean; sourcePath?: string;
   warnings?: string[]; replaceBlockIds?: string[];
@@ -115,15 +144,19 @@ export function writeManagedGuidanceBlock(files: ManagedBlockMergeFsOps, targetP
   // Without records, the plain merge as before; a refresh-only call (`onlyIfPresent`) then writes nothing.
   if (!opts.records) {
     if (opts.onlyIfPresent) return false;
-    merge();
-    return true;
+    return merge();
   }
   const existing = files.exists(targetPath) ? files.readFile(targetPath) : "";
   const decision = decideManagedBlock(existing, blockId, content, opts.records, targetPath,
     { unrecorded: opts.unrecorded ?? "refresh", onlyIfPresent: opts.onlyIfPresent, sourcePath: opts.sourcePath });
   if (decision.note) opts.warnings?.push(decision.note);
-  if (!decision.write) return false;
-  merge();
+  if (!decision.write) {
+    if (decision.standing === "edited" || decision.standing === "unrecorded") {
+      pruneKeptManagedBlock(files, targetPath, blockId, content, opts.records, opts.warnings);
+    }
+    return false;
+  }
+  if (!merge()) return false;
   recordManagedBlockWrite(opts.records, targetPath, blockId, content, opts.warnings);
   return true;
 }

packages/daemon/src/domain/managed-blocks.ts

@@ -41,15 +41,95 @@ export function managedBlockText(blockId: string, content: string): string {
 /** What `mergeManagedBlock` puts between a file's existing text and a block it adds at the end. */
 export const MANAGED_BLOCK_APPEND_SEPARATOR = "\n\n";
 
+/** A BEGIN or END marker for `blockId`, in the current or the legacy form, as an editor or formatter may leave it: any
+ *  run of whitespace, line breaks included, between its words. */
+function markerSource(kind: "BEGIN" | "END", blockId: string): string {
+  return `<!--\\s*${kind}\\s+(?:OpenRig|RIGGED)\\s+MANAGED\\s+BLOCK:\\s*${escapeRegex(blockId)}\\s*-->`;
+}
+
+/** One `blockId` block in a file: where it and its body start and end, and the text between its markers. */
+export interface FoundManagedBlock { start: number; end: number; bodyStart: number; bodyEnd: number; body: string }
+
+/** Every `blockId` block in `content`, in order: each BEGIN paired with the next marker when that marker is an END. A
+ *  marker left without a pair (an END with no BEGIN before it, or a BEGIN followed by another BEGIN or by nothing) is
+ *  counted in `unpaired`: where its block ends, or starts, can't be read. */
+export function findManagedBlocks(content: string, blockId: string): { blocks: FoundManagedBlock[]; unpaired: number } {
+  const markers = [...content.matchAll(new RegExp(`(${markerSource("BEGIN", blockId)})|${markerSource("END", blockId)}`, "g"))]
+    .map((m) => ({ begin: m[1] !== undefined, index: m.index!, length: m[0].length }));
+  const blocks: FoundManagedBlock[] = [];
+  let unpaired = 0;
+  for (let i = 0; i < markers.length; i++) {
+    const marker = markers[i]!;
+    const next = markers[i + 1];
+    if (marker.begin && next && !next.begin) {
+      const bodyStart = marker.index + marker.length;
+      blocks.push({ start: marker.index, end: next.index + next.length, bodyStart, bodyEnd: next.index, body: content.slice(bodyStart, next.index) });
+      i++;
+    } else {
+      unpaired++;
+    }
+  }
+  return { blocks, unpaired };
+}
+
+/** The note for a block OpenRig didn't write because a marker of it has lost its pair. */
+export function damagedManagedBlockNote(targetPath: string, blockId: string): string {
+  return `guidance_block_markers_damaged: ${targetPath}: ${blockId} has a BEGIN or END marker without its pair, so OpenRig `
+    + "didn't add another copy; restore the missing marker or remove the partial block, and OpenRig's next write keeps one block";
+}
+
+/**
+ * `existing` with `blockId`'s block written as `block`, or null when it can't be written without a second copy: the file
+ * has a marker of that block without its pair, and no complete copy. The first copy is replaced in place and a later copy
+ * is removed with the separator before it, so a file that collected copies keeps one; with `keepLater`, a later copy it
+ * names stays, unless it repeats one already kept. Blocks of `replaceBlockIds` (older ids) are removed. A file with none
+ * of these gets the block at its end.
+ */
+export function mergeManagedBlockText(existing: string, blockId: string, block: string, replaceBlockIds: readonly string[] = [],
+  keepLater?: (body: string) => boolean): string | null {
+  const own = findManagedBlocks(existing, blockId);
+  if (own.blocks.length === 0 && own.unpaired > 0) return null;
+  const keptLater: string[] = [];
+  const edits: Array<{ start: number; end: number; text: string }> = [];
+  own.blocks.forEach((found, i) => {
+    if (i === 0) edits.push({ start: found.start, end: found.end, text: block });
+    else if (keepLater?.(found.body) && !keptLater.some((body) => managedBlockBodyMatches(body, found.body))) keptLater.push(found.body);
+    else edits.push({ start: withSeparator(existing, found.start), end: found.end, text: "" });
+  });
+  for (const id of new Set(replaceBlockIds)) {
+    if (id === blockId) continue;
+    for (const found of findManagedBlocks(existing, id).blocks) edits.push({ start: found.start, end: found.end, text: "" });
+  }
+  if (edits.length === 0) return `${existing}${MANAGED_BLOCK_APPEND_SEPARATOR}${block}`;
+  // A block of one id inside another's is left to the outer edit.
+  const ordered: typeof edits = [];
+  for (const edit of edits.sort((a, b) => a.start - b.start)) if (edit.start >= (ordered.at(-1)?.end ?? 0)) ordered.push(edit);
+  let updated = existing;
+  // The block goes in by slicing, never a replacement string, so `$&` and the like in authored content stay as written.
+  for (const edit of ordered.reverse()) updated = `${updated.slice(0, edit.start)}${edit.text}${updated.slice(edit.end)}`;
+  if (own.blocks.length === 0) updated = `${updated.trim()}\n\n${block}`.trim();
+  // End with one newline only when the file doesn't already: re-merging on every launch must not add a line each time
+  // (#2372), and blank lines a person left after the last block stay.
+  return updated.endsWith("\n") ? updated : `${updated}\n`;
+}
+
+/** Where a later copy's removal starts: before the newlines that separate it from the text above, so removing the copy
+ *  takes the separator the writer put there. */
+function withSeparator(content: string, start: number): number {
+  let from = start;
+  while (from > 0 && content[from - 1] === "\n") from--;
+  return from;
+}
+
+/** Write `blockId`'s block into a guidance file (see `mergeManagedBlockText`). Returns false, writing nothing and naming
+ *  the block in `warnings`, when a marker of it has lost its pair. */
 export function mergeManagedBlock(
   fs: ManagedBlockMergeFsOps,
   targetPath: string,
   blockId: string,
   content: string,
   options?: MergeManagedBlockOptions,
-): void {
-  const begin = MANAGED_BLOCK_START(blockId);
-  const end = MANAGED_BLOCK_END(blockId);
+): boolean {
   const block = managedBlockText(blockId, content);
 
   if (!fs.exists(targetPath)) {
@@ -57,49 +137,39 @@ export function mergeManagedBlock(
     fs.writeFile(targetPath, block);
     const warnings = excludeNewGeneratedFiles(nodePath.dirname(targetPath), [targetPath]);
     options?.warnings?.push(...warnings);
-    return;
+    return true;
   }
 
   const existing = fs.readFile(targetPath);
-  const allReplaceIds = Array.from(new Set([blockId, ...(options?.replaceBlockIds ?? [])]));
-  const replaceableIds = allReplaceIds.filter((id) => {
-    const candidateBegin = MANAGED_BLOCK_START(id);
-    const candidateEnd = MANAGED_BLOCK_END(id);
-    const legacyBegin = LEGACY_BLOCK_START(id);
-    const legacyEnd = LEGACY_BLOCK_END(id);
-    return (
-      (existing.includes(candidateBegin) && existing.includes(candidateEnd)) ||
-      (existing.includes(legacyBegin) && existing.includes(legacyEnd))
-    );
-  });
-
-  if (replaceableIds.length > 0) {
-    let updated = existing;
-    for (const id of replaceableIds) {
-      const candidateBegin = MANAGED_BLOCK_START(id);
-      const candidateEnd = MANAGED_BLOCK_END(id);
-      const regex = new RegExp(`${escapeRegex(candidateBegin)}[\\s\\S]*?${escapeRegex(candidateEnd)}`, "g");
-      // A replacer function inserts the block literally; a replacement string
-      // would expand `$$`, `$&`, `` $` `` and `$'` in the authored content.
-      const replacement = id === blockId ? block : "";
-      updated = updated.replace(regex, () => replacement);
-      // Legacy marker variant from prior installs — replace with the
-      // OpenRig form (or strip when not the active block id).
-      const legacyBegin = LEGACY_BLOCK_START(id);
-      const legacyEnd = LEGACY_BLOCK_END(id);
-      const legacyRegex = new RegExp(`${escapeRegex(legacyBegin)}[\\s\\S]*?${escapeRegex(legacyEnd)}`, "g");
-      updated = updated.replace(legacyRegex, () => replacement);
-    }
-    if (!updated.includes(begin) || !updated.includes(end)) {
-      updated = `${updated.trim()}\n\n${block}`.trim();
-    }
-    // End with one newline only when the file doesn't already: re-merging on every launch must not add a line each time
-    // (#2372), and blank lines a person left after the last block stay.
-    fs.writeFile(targetPath, updated.endsWith("\n") ? updated : `${updated}\n`);
-    return;
+  const merged = mergeManagedBlockText(existing, blockId, block, options?.replaceBlockIds ?? []);
+  if (merged === null) {
+    options?.warnings?.push(damagedManagedBlockNote(targetPath, blockId));
+    return false;
   }
+  fs.writeFile(targetPath, merged);
+  if (findManagedBlocks(existing, blockId).unpaired > 0) options?.warnings?.push(unpairedMarkerNote(targetPath, blockId));
+  return true;
+}
 
-  fs.writeFile(targetPath, `${existing}${MANAGED_BLOCK_APPEND_SEPARATOR}${block}`);
+/** The note for a marker without its pair left beside a block that was written. */
+export function unpairedMarkerNote(targetPath: string, blockId: string): string {
+  return `guidance_block_marker_unpaired: ${targetPath}: ${blockId} was written, and a BEGIN or END marker of it without its `
+    + "pair was left as it is; remove it or restore its pair";
+}
+
+/** `content` with each `blockId` block whose markers an editor rewrapped written back in OpenRig's own form, its body
+ *  exactly as it is. Markers already in the current or legacy form stay as they are. */
+export function withCanonicalMarkers(content: string, blockId: string): string {
+  let updated = content;
+  for (const found of findManagedBlocks(content, blockId).blocks.reverse()) {
+    const begin = content.slice(found.start, found.bodyStart);
+    const end = content.slice(found.bodyEnd, found.end);
+    const exact = (begin === MANAGED_BLOCK_START(blockId) && end === MANAGED_BLOCK_END(blockId))
+      || (begin === LEGACY_BLOCK_START(blockId) && end === LEGACY_BLOCK_END(blockId));
+    if (exact) continue;
+    updated = `${updated.slice(0, found.start)}${MANAGED_BLOCK_START(blockId)}${found.body}${MANAGED_BLOCK_END(blockId)}${updated.slice(found.end)}`;
+  }
+  return updated;
 }
 
 /** Each `blockId` block in `content` (current markers): the whole block and the text between its markers. */
@@ -136,19 +206,47 @@ export function managedBlockOpenings(content: string, blockId: string): number {
  *  - `current`: it holds the source's text;
  *  - `stale`: it holds what OpenRig last wrote, and the source has changed since, so it's OpenRig's to refresh;
  *  - `edited`: it holds something else, which someone wrote by hand;
- *  - `unrecorded`: it differs from the source and OpenRig has no record of writing it, so which of the two is unknown.
+ *  - `unrecorded`: it differs from the source and OpenRig has no record of writing it, so which of the two is unknown;
+ *  - `damaged`: it holds a marker of the block without its pair, and no complete copy, so the block can't be read.
  *  A block written more than once counts as edited when any copy is. */
-export type ManagedBlockStanding = "absent" | "current" | "stale" | "edited" | "unrecorded";
+export type ManagedBlockStanding = "absent" | "current" | "stale" | "edited" | "unrecorded" | "damaged";
 
 export function managedBlockStanding(content: string, blockId: string, source: string, recordedHash: string | undefined,
   hash: (body: string) => string): ManagedBlockStanding {
-  const bodies = managedBlockBodies(content, blockId);
-  if (bodies.length === 0) return "absent";
+  const found = findManagedBlocks(content, blockId);
+  const bodies = found.blocks.map((block) => block.body);
+  if (bodies.length === 0) return found.unpaired > 0 ? "damaged" : "absent";
   if (bodies.every((body) => managedBlockBodyMatches(body, source))) return "current";
   if (recordedHash === undefined) return "unrecorded";
   return bodies.every((body) => hash(body) === recordedHash) ? "stale" : "edited";
 }
 
+/** `content` with the extra copies of a `blockId` block taken out where no one's text is lost: a later copy whose body
+ *  repeats an earlier copy's, and, beside a copy that's kept, a copy that `isOpenRigs` says holds only what OpenRig
+ *  wrote. Every other copy stays where it is. Null when there's nothing to take out. */
+export function pruneManagedBlockCopies(content: string, blockId: string, isOpenRigs: (body: string) => boolean): string | null {
+  const { blocks } = findManagedBlocks(content, blockId);
+  if (blocks.length < 2) return null;
+  const kept: FoundManagedBlock[] = [];
+  const removed: FoundManagedBlock[] = [];
+  for (const block of blocks) {
+    if (kept.some((other) => managedBlockBodyMatches(other.body, block.body))) removed.push(block);
+    else kept.push(block);
+  }
+  const people = kept.filter((block) => !isOpenRigs(block.body));
+  if (people.length > 0) for (const block of kept.filter((b) => isOpenRigs(b.body))) removed.push(block);
+  if (removed.length === 0) return null;
+  let updated = content;
+  for (const block of removed.sort((a, b) => b.start - a.start)) {
+    // A copy goes with the newlines before it; one that starts the file goes with the newlines after it instead.
+    const from = withSeparator(content, block.start);
+    let to = block.end;
+    if (from === 0) while (updated[to] === "\n") to++;
+    updated = `${updated.slice(0, from)}${updated.slice(to)}`;
+  }
+  return updated;
+}
+
 /** Whether `content` holds a `blockId` block whose body is anything but `written`: someone edited it. */
 export function hasEditedManagedBlock(content: string, blockId: string, written: string): boolean {
   return [...content.matchAll(managedBlockPattern(blockId))].some((m) => !managedBlockBodyMatches(m[1]!, written));

packages/daemon/src/domain/package-install-service.ts

@@ -8,7 +8,7 @@ import { detectConflicts } from "./conflict-detector.js";
 import { applyPolicy } from "./install-policy.js";
 
 export type PackageInstallOutcome =
-  | { ok: true; installId: string; packageId: string; applied: number; deferred: number }
+  | { ok: true; installId: string; packageId: string; applied: number; deferred: number; notes?: string[] }
   | { ok: false; code: "conflict_blocked"; message: string }
   | { ok: false; code: "policy_rejected"; message: string }
   | { ok: false; code: "manifest_hash_mismatch"; message: string }
@@ -101,7 +101,7 @@ export class PackageInstallService {
     }
 
     // Verify
-    const verification = this.installVerifier.verify(result.installId);
+    const verification = this.installVerifier.verify(result.installId, { skipped: result.notes?.length ?? 0 });
     if (!verification.passed) {
       return { ok: false, code: "verification_failed", message: "Post-apply verification failed" };
     }
@@ -112,6 +112,7 @@ export class PackageInstallService {
       packageId: pkg.id,
       applied: result.applied.length,
       deferred: result.deferred.length,
+      ...(result.notes?.length ? { notes: result.notes } : {}),
     };
   }
 }

packages/daemon/src/domain/restore-guidance.ts

@@ -17,25 +17,21 @@ import nodePath from "node:path";
 import { lstatSync } from "node:fs";
 import type Database from "better-sqlite3";
 import {
-  MANAGED_BLOCK_START,
-  MANAGED_BLOCK_END,
   DEFAULT_CLAUDE_MANAGED_BLOCK_FILE,
+  findManagedBlocks,
   mergeManagedBlock,
   stripManagedBlocks,
   type ManagedBlockMergeFsOps,
   isPerSeatRoleGuidance,
   isPerSeatRoleStartupFile,
 } from "./managed-blocks.js";
-import { decideManagedBlock, recordManagedBlockWrite, type ManagedBlockRecords } from "./managed-block-records.js";
+import { decideManagedBlock, pruneKeptManagedBlock, recordManagedBlockWrite, type ManagedBlockRecords } from "./managed-block-records.js";
 import { resolveConcreteHint } from "./runtime-adapter.js";
 import { reanchorBuiltinStartupFile, reanchorShippedProjectionEntry, withContextEntryFloor } from "./builtin-startup-files.js";
 import type { NodeStartupSnapshot } from "./types.js";
 import { SEAT_SKILLS_BOOTSTRAP_BLOCK_ID } from "./seat-skill-storage.js";
 import { guidanceFileIsLink } from "./footprint-choice.js";
 
-const LEGACY_BLOCK_START = (id: string) => `<!-- BEGIN RIGGED MANAGED BLOCK: ${id} -->`;
-const LEGACY_BLOCK_END = (id: string) => `<!-- END RIGGED MANAGED BLOCK: ${id} -->`;
-
 
 export interface GuidanceItem {
   blockId: string;
@@ -97,15 +93,10 @@ export function recordedGuidanceFile(db: Pick<Database.Database, "prepare">, nod
   } catch { return null; }
 }
 
-/** Whether guidance text holds this id's block as it is written: a BEGIN marker followed later by its END, in the
- *  current or legacy form. For reporting an installed file; restore's own `blockState` is unchanged. */
+/** Whether guidance text holds this id's block as it is written: a BEGIN marker followed by its END, in the current or
+ *  legacy form, read as the writer reads it (`findManagedBlocks`). For reporting an installed file. */
 export function hasCompleteGuidanceBlock(content: string, blockId: string): boolean {
-  const ordered = (start: string, end: string): boolean => {
-    const begin = content.indexOf(start);
-    return begin >= 0 && content.indexOf(end, begin + start.length) >= 0;
-  };
-  return ordered(MANAGED_BLOCK_START(blockId), MANAGED_BLOCK_END(blockId))
-    || ordered(LEGACY_BLOCK_START(blockId), LEGACY_BLOCK_END(blockId));
+  return findManagedBlocks(content, blockId).blocks.length > 0;
 }
 
 /** The guidance file a seat's managed blocks live in, and the blocks it should hold on restore. */
@@ -199,14 +190,13 @@ export function applySeatSkillsLineRule(guidance: SeatGuidance, answeredYes: boo
 
 type BlockState = "complete" | "absent" | "incomplete";
 
-/** A block counts only with both its markers (current or legacy form). A lone marker is incomplete:
- *  writing next to it is unsafe, because cleanup strips from a BEGIN to the next END. */
+/** A block counts only with both its markers (current or legacy form), read as the writer reads them. A lone marker is
+ *  incomplete: writing next to it is unsafe, because cleanup strips from a BEGIN to the next END, and it would add a
+ *  second copy beside one that can't be read. */
 function blockState(content: string, blockId: string): BlockState {
-  const current = [content.includes(MANAGED_BLOCK_START(blockId)), content.includes(MANAGED_BLOCK_END(blockId))];
-  const legacy = [content.includes(LEGACY_BLOCK_START(blockId)), content.includes(LEGACY_BLOCK_END(blockId))];
-  if ((current[0] && current[1]) || (legacy[0] && legacy[1])) return "complete";
-  if (current[0] || current[1] || legacy[0] || legacy[1]) return "incomplete";
-  return "absent";
+  const found = findManagedBlocks(content, blockId);
+  if (found.blocks.length > 0) return "complete";
+  return found.unpaired > 0 ? "incomplete" : "absent";
 }
 
 function blockStates(guidance: SeatGuidance, fs: Pick<ManagedBlockMergeFsOps, "exists" | "readFile">): Map<string, BlockState> {
@@ -228,11 +218,13 @@ export interface GuidanceRepair {
   refreshed: string[];
   /** #2456: blocks left as they are although they differ from their source, each named with the reason
    *  (`guidance_block_edited`, `guidance_block_may_be_stale` or `guidance_block_record_unreadable`). The seat runs them as
-   *  they are. A block written whose record wasn't saved is named here too (`guidance_block_record_not_saved`). */
+   *  they are. A block written whose record wasn't saved is named here too (`guidance_block_record_not_saved`), and so are
+   *  a kept block's removed repeats (`guidance_block_copies_removed`). */
   kept: string[];
 }
 
-const KEPT_GUIDANCE_PREFIXES = ["guidance_block_edited: ", "guidance_block_may_be_stale: ", "guidance_block_record_unreadable: "];
+const KEPT_GUIDANCE_PREFIXES = ["guidance_block_edited: ", "guidance_block_may_be_stale: ", "guidance_block_record_unreadable: ",
+  "guidance_block_markers_damaged: "];
 
 /** #2456: the one line a seat is told when a managed guidance block was left as it is (edited by hand, or possibly stale),
  *  naming each one, or undefined when none was. */
@@ -261,7 +253,8 @@ export function appendIsCleanupSafe(content: string, blocks: Array<{ blockId: st
 
 /** Put back the missing managed guidance blocks. With `records` (#2456), a block already there that OpenRig wrote is
  *  refreshed from its changed source, and one edited since, or with no record, is kept and named (`decideManagedBlock`).
- *  Without them a block already there is left as it is, as before. Any other text in the file is left exactly as it is,
+ *  Without them a block already there keeps its text. Either way a block left in place loses its exact repeats, and
+ *  OpenRig's own copies beside an edited one, and rewrapped markers go back to OpenRig's form (`pruneKeptManagedBlock`). Any other text in the file is left exactly as it is,
  *  and nothing is written unless cleanup would later remove exactly what was written. Never throws: a failure becomes a
  *  reported gap. */
 export function restoreMissingGuidance(guidance: SeatGuidance, fs: ManagedBlockMergeFsOps, records?: ManagedBlockRecords): GuidanceRepair {
@@ -279,17 +272,27 @@ export function restoreMissingGuidance(guidance: SeatGuidance, fs: ManagedBlockM
   for (const item of guidance.items) {
     const state = states.get(item.blockId);
     if (state === "complete") {
-      if (!records || item.unresolved) continue;
+      if (item.unresolved) continue;
       let source: string;
       try {
         if (!fs.exists(item.sourcePath)) continue;
         source = fs.readFile(item.sourcePath);
       } catch { continue; }
+      // Without records the block's text stays as it is; only its exact repeats and rewrapped markers are tidied.
+      if (!records) {
+        pruneKeptManagedBlock(fs, guidance.targetPath, item.blockId, source, undefined, repair.kept);
+        continue;
+      }
       // #2456: the same decision every adapter's guidance write makes; an exact resume and a handover keep an unrecorded block.
       const decision = decideManagedBlock(existing ?? "", item.blockId, source, records, guidance.targetPath, { unrecorded: "keep", sourcePath: item.sourcePath });
       if (decision.note) repair.kept.push(decision.note);
-      else if (decision.standing === "current") recordManagedBlockWrite(records, guidance.targetPath, item.blockId, source, repair.kept);
-      else if (decision.write) toWrite.push({ blockId: item.blockId, content: source, refresh: true });
+      if (decision.write && decision.standing !== "current") {
+        toWrite.push({ blockId: item.blockId, content: source, refresh: true });
+        continue;
+      }
+      if (decision.standing === "current") recordManagedBlockWrite(records, guidance.targetPath, item.blockId, source, repair.kept);
+      // A block left as it is (current, edited or unrecorded) keeps one copy of each distinct text, in OpenRig's markers.
+      pruneKeptManagedBlock(fs, guidance.targetPath, item.blockId, source, records, repair.kept);
       continue;
     }
     if (state === "incomplete") {
@@ -313,6 +316,9 @@ export function restoreMissingGuidance(guidance: SeatGuidance, fs: ManagedBlockM
   if (toWrite.length === 0) return repair;
   // A file that doesn't exist yet holds no text to lose. An existing one is written only if the
   // next rig down would remove exactly what is added.
+  // Read again: removing a kept block's repeats above may have changed the file.
+  try { existing = fs.exists(guidance.targetPath) ? fs.readFile(guidance.targetPath) : null; }
+  catch (err) { repair.gaps.push(`could not read ${guidance.targetPath}: ${(err as Error).message}`); return repair; }
   if (existing !== null && !appendIsCleanupSafe(existing, toWrite)) {
     for (const block of toWrite) {
       repair.gaps.push(`${block.blockId}: not written, because ${guidance.targetPath} has a managed-block marker that the next rig down would strip together with other text, so adding blocks there could cost that text`);
@@ -321,7 +327,7 @@ export function restoreMissingGuidance(guidance: SeatGuidance, fs: ManagedBlockM
   }
   for (const block of toWrite) {
     try {
-      mergeManagedBlock(fs, guidance.targetPath, block.blockId, block.content);
+      if (!mergeManagedBlock(fs, guidance.targetPath, block.blockId, block.content, { warnings: repair.gaps })) continue;
       if (records) recordManagedBlockWrite(records, guidance.targetPath, block.blockId, block.content, repair.kept);
       (block.refresh ? repair.refreshed : repair.restored).push(block.blockId);
     } catch (err) {

packages/daemon/src/routes/packages.ts

@@ -273,7 +273,7 @@ packagesRoutes.post("/install", async (c) => {
   }
 
   // Verify
-  const verification = installVerifier.verify(result.installId);
+  const verification = installVerifier.verify(result.installId, { skipped: result.notes?.length ?? 0 });
   if (!verification.passed) {
     eventBus.emit({ type: "package.install_failed", packageName: resolved.manifest.name, code: "verification_failed", message: "Post-apply verification failed" });
     return c.json({
@@ -281,6 +281,7 @@ packagesRoutes.post("/install", async (c) => {
       code: "verification_failed",
       installId: result.installId,
       verification,
+      ...(result.notes?.length ? { notes: result.notes } : {}),
     }, 500);
   }
 
@@ -302,6 +303,7 @@ packagesRoutes.post("/install", async (c) => {
     conflicts: result.conflicts,
     verification,
     ...(policyResult.rejected.length > 0 ? { policyRejected: policyResult.rejected } : {}),
+    ...(result.notes?.length ? { notes: result.notes } : {}),
   }, 201);
 });
 

packages/daemon/test/bootstrap-orchestrator.test.ts

@@ -1387,6 +1387,38 @@ exports:
     expect(result.errors.some((e) => e.includes("skipped"))).toBe(true);
   });
 
+  it("a package whose only guidance entry is left as it is still imports the rig, with the note in warnings", async () => {
+    writePkg(path.join(tmpDir, "test-pkg"), VALID_MANIFEST_YAML, { "skills/helper/SKILL.md": "# Helper" });
+    const guidanceManifest = `
+schema_version: 1
+name: guidance-pkg
+version: "1.0.0"
+summary: Guidance only
+compatibility:
+  runtimes: [claude-code]
+exports:
+  guidance:
+    - source: guidance/rules.md
+      name: rules
+      kind: claude_md
+      supported_scopes: [project_shared]
+      default_scope: project_shared
+      merge_strategy: managed_block
+`.trim();
+    writePkg(path.join(tmpDir, "guidance-pkg"), guidanceManifest, { "guidance/rules.md": "Follow these rules." });
+    const damaged = "# Project\n\n<!-- BEGIN OpenRig MANAGED BLOCK: guidance-pkg -->\nhalf a block\n";
+    fs.writeFileSync(path.join(tmpDir, "CLAUDE.md"), damaged);
+    const specPath = writeSpec(SPEC_WITH_PACKAGES_YAML.replace("      - ./test-pkg", "      - ./test-pkg\n      - ./guidance-pkg"));
+
+    const result = await buildOrchestrator().bootstrap({ mode: "apply", sourceRef: specPath, autoApprove: true });
+
+    expect(fs.readFileSync(path.join(tmpDir, "CLAUDE.md"), "utf-8")).toBe(damaged);
+    expect(result.errors).toEqual([]);
+    expect(result.status).toBe("completed");
+    expect(result.stages.find((s) => s.stage === "import_rig")?.status).not.toBe("skipped");
+    expect(result.warnings).toContainEqual(expect.stringMatching(/^Package '\.\/guidance-pkg' \(claude-code\): guidance_block_markers_damaged: .*CLAUDE\.md: guidance-pkg has a BEGIN or END marker without its pair/));
+  });
+
   // === P7-T05: Bundle source tests ===
 
   // T25: Real bundle bootstrap happy path

packages/daemon/test/install-engine.test.ts

@@ -234,6 +234,48 @@ describe("InstallEngine", () => {
     expect(fs.readFileSync(targetPath, "utf8")).toBe(`${prefix}<!-- BEGIN OpenRig MANAGED BLOCK: test-pkg -->\nUpdated guidance.\n<!-- END OpenRig MANAGED BLOCK: test-pkg -->\n# Footer\n`);
   });
 
+  it("keeps one copy of its block: the first is updated in place and the repeats go", () => {
+    const pkg = seedPackage();
+    const sourcePath = writeSource("guidance/AGENTS.md", "Updated guidance.");
+    const targetPath = path.join(repoRoot, "AGENTS.md");
+    const old = "<!-- BEGIN OpenRig MANAGED BLOCK: test-pkg -->\nOld content.\n<!-- END OpenRig MANAGED BLOCK: test-pkg -->";
+    fs.writeFileSync(targetPath, `# Header\n\n${old}\n\n${old}\n# Footer\n`);
+    const entry = makeEntry({ exportType: "guidance", classification: "managed_merge", targetPath, sourcePath });
+    new InstallEngine(installRepo, realFs(tmpDir)).apply(makePolicy([entry]), makePlan([entry]), pkg.id, repoRoot);
+    expect(fs.readFileSync(targetPath, "utf8")).toBe(
+      "# Header\n\n<!-- BEGIN OpenRig MANAGED BLOCK: test-pkg -->\nUpdated guidance.\n<!-- END OpenRig MANAGED BLOCK: test-pkg -->\n# Footer\n");
+  });
+
+  it("keeps a later copy someone edited, and every different edit, with the text between", () => {
+    const pkg = seedPackage();
+    const sourcePath = writeSource("guidance/AGENTS.md", "Updated guidance.");
+    const targetPath = path.join(repoRoot, "AGENTS.md");
+    const copy = (body: string) => `<!-- BEGIN OpenRig MANAGED BLOCK: test-pkg -->\n${body}\n<!-- END OpenRig MANAGED BLOCK: test-pkg -->`;
+    fs.writeFileSync(targetPath, `# Header\n\n${copy("Old content.")}\n\nmine\n\n${copy("Old content, with my rule.")}\n\n${copy("Another edit.")}\n`);
+    const entry = makeEntry({ exportType: "guidance", classification: "managed_merge", targetPath, sourcePath });
+    new InstallEngine(installRepo, realFs(tmpDir)).apply(makePolicy([entry]), makePlan([entry]), pkg.id, repoRoot);
+    expect(fs.readFileSync(targetPath, "utf8")).toBe(
+      `# Header\n\n${copy("Updated guidance.")}\n\nmine\n\n${copy("Old content, with my rule.")}\n\n${copy("Another edit.")}\n`);
+  });
+
+  it("installs the rest when a guidance block lost its END: that file is left as it is and named, with no copy added", () => {
+    const pkg = seedPackage();
+    const skillSource = writeSource("skills/foo/SKILL.md", "# Foo Skill");
+    const skillTarget = path.join(repoRoot, ".agents/skills/foo/SKILL.md");
+    const guidanceSource = writeSource("guidance/AGENTS.md", "Updated guidance.");
+    const guidanceTarget = path.join(repoRoot, "AGENTS.md");
+    const text = "# Header\n<!-- BEGIN OpenRig MANAGED BLOCK: test-pkg -->\nOld content.\n# Footer\n";
+    fs.writeFileSync(guidanceTarget, text);
+    const skill = makeEntry({ exportName: "foo", targetPath: skillTarget, sourcePath: skillSource });
+    const guidance = makeEntry({ exportType: "guidance", classification: "managed_merge", targetPath: guidanceTarget, sourcePath: guidanceSource });
+    const result = new InstallEngine(installRepo, realFs(tmpDir)).apply(makePolicy([skill, guidance]), makePlan([skill, guidance]), pkg.id, repoRoot);
+    expect(fs.readFileSync(guidanceTarget, "utf8")).toBe(text);
+    expect(fs.readFileSync(skillTarget, "utf8")).toBe("# Foo Skill");
+    expect(result.applied.map((e) => e.targetPath)).toEqual([skillTarget]);
+    expect(result.notes).toEqual([expect.stringMatching(/^guidance_block_markers_damaged: .*AGENTS\.md: test-pkg has a BEGIN or END marker without its pair/)]);
+    expect(installRepo.getInstall(result.installId)?.status).toBe("applied");
+  });
+
   // Test 7: Backup created before overwrite
   it("backup created before overwrite", () => {
     const pkg = seedPackage();

packages/daemon/test/managed-blocks-one-copy.test.ts

@@ -0,0 +1,195 @@
+// A guidance file keeps exactly one copy of each OpenRig-managed block, however often OpenRig writes it: after an editor
+// or formatter touched its markers, after copies collected, and when a marker lost its pair. A person's edit is kept.
+import { describe, expect, it } from "vitest";
+import {
+  managedBlockStanding,
+  managedBlockText,
+  mergeManagedBlock,
+  type ManagedBlockMergeFsOps,
+} from "../src/domain/managed-blocks.js";
+import { managedBlockBodyHash, writeManagedGuidanceBlock, type ManagedBlockRecords } from "../src/domain/managed-block-records.js";
+import { restoreMissingGuidance } from "../src/domain/restore-guidance.js";
+
+const FILE = "/repo/AGENTS.md";
+const SOURCE = "/specs/culture.md";
+
+/** An in-memory guidance file and source, so nothing here touches a real instruction file. */
+function memory(files: Record<string, string>): ManagedBlockMergeFsOps & { files: Record<string, string> } {
+  return {
+    files,
+    exists: (p) => p in files,
+    readFile: (p) => files[p]!,
+    writeFile: (p, content) => { files[p] = content; },
+  };
+}
+
+function recordsOf(entries: Record<string, string> = {}): ManagedBlockRecords & { entries: Record<string, string> } {
+  return {
+    entries,
+    get: (file, id) => entries[`${file}#${id}`],
+    set: (file, id, body) => { entries[`${file}#${id}`] = managedBlockBodyHash(body); },
+  };
+}
+
+const count = (text: string, id = "CULTURE.md") => text.split(`<!-- BEGIN OpenRig MANAGED BLOCK: ${id} -->`).length - 1;
+
+describe("the writer keeps one copy", () => {
+  it("reads markers a formatter rewrapped as the block, and replaces it in place at every launch", () => {
+    const touched = "# Notes\n\n<!--\n  BEGIN OpenRig MANAGED BLOCK: CULTURE.md\n-->\nold culture\n<!--   END OpenRig  MANAGED BLOCK:  CULTURE.md -->\n\nafter\n";
+    const fs = memory({ [FILE]: touched });
+    const sizes: number[] = [];
+    const written: unknown[] = [];
+    for (let launch = 0; launch < 4; launch++) {
+      written.push(mergeManagedBlock(fs, FILE, "CULTURE.md", "new culture"));
+      sizes.push(fs.files[FILE]!.length);
+    }
+    expect(fs.files[FILE]).toBe(`# Notes\n\n${managedBlockText("CULTURE.md", "new culture")}\n\nafter\n`);
+    expect(new Set(sizes).size).toBe(1);
+    expect(written).toEqual([true, true, true, true]);
+  });
+
+  it("collapses copies that collected to the first, and keeps a person's text before, between and after them", () => {
+    const block = managedBlockText("CULTURE.md", "culture");
+    const fs = memory({ [FILE]: `# Notes\n\n${block}\n\nperson text\n\n${block}\n\n${block}\n\nthe end\n` });
+    mergeManagedBlock(fs, FILE, "CULTURE.md", "culture");
+    expect(fs.files[FILE]).toBe(`# Notes\n\n${block}\n\nperson text\n\nthe end\n`);
+  });
+
+  it.each([
+    ["a BEGIN whose END was lost", "# Notes\n\n<!-- BEGIN OpenRig MANAGED BLOCK: CULTURE.md -->\nculture\n<!-- END OpenRig MANAGED BLOCK -->\n"],
+    ["an END whose BEGIN was lost", "# Notes\n\n<!-- BEGIN MANAGED BLOCK: CULTURE.md -->\nculture\n<!-- END OpenRig MANAGED BLOCK: CULTURE.md -->\n"],
+  ])("adds no copy beside %s, at any launch, and names it", (_name, text) => {
+    const fs = memory({ [FILE]: text });
+    const warnings: string[] = [];
+    const written: unknown[] = [];
+    for (let launch = 0; launch < 3; launch++) written.push(mergeManagedBlock(fs, FILE, "CULTURE.md", "culture", { warnings }));
+    expect(fs.files[FILE]).toBe(text);
+    expect(warnings).toHaveLength(3);
+    expect(written).toEqual([false, false, false]);
+    expect(warnings[0]).toMatch(/^guidance_block_markers_damaged: \/repo\/AGENTS\.md: CULTURE\.md has a BEGIN or END marker without its pair/);
+  });
+
+  it("still replaces a complete copy when a lost marker sits beside it, leaves that marker, and names it", () => {
+    const lone = "<!-- BEGIN OpenRig MANAGED BLOCK: CULTURE.md -->\nstray\n";
+    const fs = memory({ [FILE]: `${lone}\n${managedBlockText("CULTURE.md", "old")}\n` });
+    const warnings: string[] = [];
+    const written = mergeManagedBlock(fs, FILE, "CULTURE.md", "new", { warnings });
+    expect(fs.files[FILE]).toBe(`${lone}\n${managedBlockText("CULTURE.md", "new")}\n`);
+    expect(written).toBe(true);
+    expect(warnings).toEqual([expect.stringMatching(/^guidance_block_marker_unpaired: \/repo\/AGENTS\.md: CULTURE\.md was written/)]);
+  });
+
+  it("appends to a file with no marker at all, as before", () => {
+    const fs = memory({ [FILE]: "# Notes\n" });
+    mergeManagedBlock(fs, FILE, "CULTURE.md", "culture");
+    expect(fs.files[FILE]).toBe(`# Notes\n\n\n${managedBlockText("CULTURE.md", "culture")}`);
+  });
+
+  it("reads a lost marker as damaged, not absent", () => {
+    expect(managedBlockStanding("<!-- BEGIN OpenRig MANAGED BLOCK: CULTURE.md -->\nculture\n", "CULTURE.md", "culture", undefined, managedBlockBodyHash))
+      .toBe("damaged");
+    expect(managedBlockStanding("# no block\n", "CULTURE.md", "culture", undefined, managedBlockBodyHash)).toBe("absent");
+  });
+});
+
+describe("a launch's guidance write keeps a person's edit and drops only repeats", () => {
+  const launch = (fs: ManagedBlockMergeFsOps, records: ManagedBlockRecords, source: string, warnings: string[]) =>
+    writeManagedGuidanceBlock(fs, FILE, "CULTURE.md", source, { records, sourcePath: SOURCE, warnings });
+
+  it("refreshes OpenRig's own copies to one", () => {
+    const old = managedBlockText("CULTURE.md", "old culture");
+    const fs = memory({ [FILE]: `# Notes\n\n${old}\n\n${old}\n` });
+    const records = recordsOf({ [`${FILE}#CULTURE.md`]: managedBlockBodyHash("old culture") });
+    expect(launch(fs, records, "new culture", [])).toBe(true);
+    expect(fs.files[FILE]).toBe(`# Notes\n\n${managedBlockText("CULTURE.md", "new culture")}\n`);
+  });
+
+  it("keeps copies a formatter changed as edits, and leaves one of them", () => {
+    const formatted = managedBlockText("CULTURE.md", "- culture, reformatted");
+    const fs = memory({ [FILE]: `# Notes\n\n${formatted}\n\n${formatted}\n\n${formatted}\n` });
+    const records = recordsOf({ [`${FILE}#CULTURE.md`]: managedBlockBodyHash("* culture") });
+    const warnings: string[] = [];
+    expect(launch(fs, records, "* culture", warnings)).toBe(false);
+    expect(fs.files[FILE]).toBe(`# Notes\n\n${formatted}\n`);
+    expect(warnings.map((w) => w.split(":")[0])).toEqual(["guidance_block_edited", "guidance_block_copies_removed"]);
+  });
+
+  it("keeps a person's edited copy and drops OpenRig's unedited copy beside it", () => {
+    const edited = managedBlockText("CULTURE.md", "culture, with my change");
+    const fs = memory({ [FILE]: `${managedBlockText("CULTURE.md", "culture")}\n\n${edited}\n` });
+    const records = recordsOf({ [`${FILE}#CULTURE.md`]: managedBlockBodyHash("culture") });
+    expect(launch(fs, records, "culture", [])).toBe(false);
+    expect(fs.files[FILE]).toBe(`${edited}\n`);
+  });
+
+  it("keeps two different edited copies: it can't tell which one is meant", () => {
+    const text = `${managedBlockText("CULTURE.md", "edit one")}\n\n${managedBlockText("CULTURE.md", "edit two")}\n`;
+    const fs = memory({ [FILE]: text });
+    expect(launch(fs, recordsOf({ [`${FILE}#CULTURE.md`]: managedBlockBodyHash("culture") }), "culture", [])).toBe(false);
+    expect(fs.files[FILE]).toBe(text);
+  });
+
+  it("records nothing and adds no copy beside a lost marker", () => {
+    const text = "<!-- BEGIN OpenRig MANAGED BLOCK: CULTURE.md -->\nculture\n";
+    const fs = memory({ [FILE]: text });
+    const records = recordsOf();
+    const warnings: string[] = [];
+    const written: unknown[] = [];
+    for (let i = 0; i < 3; i++) written.push(launch(fs, records, "culture", warnings));
+    expect(fs.files[FILE]).toBe(text);
+    expect(written).toEqual([false, false, false]);
+    expect(records.entries).toEqual({});
+    expect(warnings.every((w) => w.startsWith("guidance_block_markers_damaged: "))).toBe(true);
+  });
+
+  it("keeps going when the file can't be written: the edited block is kept as decided, and the tidy is named", () => {
+    const formatted = managedBlockText("CULTURE.md", "- culture, reformatted");
+    const text = `${formatted}\n\n${formatted}\n`;
+    const fs = memory({ [FILE]: text });
+    fs.writeFile = () => { throw new Error("EACCES: permission denied"); };
+    const warnings: string[] = [];
+    expect(launch(fs, recordsOf({ [`${FILE}#CULTURE.md`]: managedBlockBodyHash("* culture") }), "* culture", warnings)).toBe(false);
+    expect(fs.files[FILE]).toBe(text);
+    expect(warnings.map((w) => w.split(":")[0])).toEqual(["guidance_block_edited", "guidance_block_copies_not_removed"]);
+  });
+});
+
+describe("restore keeps one copy", () => {
+  it("removes repeats of a current block, and a second restore changes nothing", () => {
+    const current = managedBlockText("CULTURE.md", "* culture");
+    const fs = memory({ [FILE]: `# Notes\n\n${current}\n\nmine\n\n${current}\n`, [SOURCE]: "* culture" });
+    const records = recordsOf({ [`${FILE}#CULTURE.md`]: managedBlockBodyHash("* culture") });
+    const guidance = { targetPath: FILE, items: [{ blockId: "CULTURE.md", sourcePath: SOURCE }] };
+    restoreMissingGuidance(guidance, fs, records);
+    const once = fs.files[FILE];
+    restoreMissingGuidance(guidance, fs, records);
+    expect(once).toBe(`# Notes\n\n${current}\n\nmine\n`);
+    expect(fs.files[FILE]).toBe(once);
+  });
+
+  it("without write records keeps the block's text, and still removes its exact repeats and puts rewrapped markers back", () => {
+    const rewrapped = "<!--\n BEGIN OpenRig MANAGED BLOCK: CULTURE.md -->\nmy edit\n<!-- END OpenRig MANAGED BLOCK: CULTURE.md -->";
+    const fs = memory({ [FILE]: `${rewrapped}\n\n${managedBlockText("CULTURE.md", "my edit")}\n`, [SOURCE]: "* culture" });
+    restoreMissingGuidance({ targetPath: FILE, items: [{ blockId: "CULTURE.md", sourcePath: SOURCE }] }, fs);
+    expect(fs.files[FILE]).toBe(`${managedBlockText("CULTURE.md", "my edit")}\n`);
+  });
+
+  it("removes a kept block's repeats, and puts back nothing beside a lost marker", () => {
+    const formatted = managedBlockText("CULTURE.md", "- culture, reformatted");
+    const fs = memory({
+      [FILE]: `# Notes\n\n${formatted}\n\n${formatted}\n\n<!-- BEGIN OpenRig MANAGED BLOCK: ROLE.md -->\nrole\n`,
+      [SOURCE]: "* culture",
+      "/specs/role.md": "role",
+    });
+    const records = recordsOf({ [`${FILE}#CULTURE.md`]: managedBlockBodyHash("* culture") });
+    const repair = restoreMissingGuidance({ targetPath: FILE, items: [
+      { blockId: "CULTURE.md", sourcePath: SOURCE },
+      { blockId: "ROLE.md", sourcePath: "/specs/role.md" },
+    ] }, fs, records);
+    expect(fs.files[FILE]).toBe(`# Notes\n\n${formatted}\n\n<!-- BEGIN OpenRig MANAGED BLOCK: ROLE.md -->\nrole\n`);
+    expect(count(fs.files[FILE]!)).toBe(1);
+    expect(repair.restored).toEqual([]);
+    expect(repair.gaps.join("\n")).toContain("ROLE.md: /repo/AGENTS.md holds only part of this block");
+    expect(repair.kept.map((k) => k.split(":")[0])).toEqual(["guidance_block_edited", "guidance_block_copies_removed"]);
+  });
+});

packages/daemon/test/packages-routes.test.ts

@@ -322,6 +322,32 @@ roles:
     expect(claudeMd).toContain("# Existing content");
   });
 
+  it("POST /api/packages/install whose only guidance entry is left as it is → 201 with the note, verified", async () => {
+    writePkg(pkgDir, GUIDANCE_MANIFEST_YAML, {
+      "guidance/rules.md": "Follow these rules.",
+    });
+    const damaged = "# Existing content\n\n<!-- BEGIN OpenRig MANAGED BLOCK: guidance-pkg -->\nhalf a block\n";
+    fs.writeFileSync(path.join(targetDir, "CLAUDE.md"), damaged);
+
+    const res = await app.request("/api/packages/install", {
+      method: "POST",
+      headers: { "Content-Type": "application/json" },
+      body: JSON.stringify({
+        sourceRef: pkgDir,
+        targetRoot: targetDir,
+        runtime: "claude-code",
+        allowMerge: true,
+      }),
+    });
+
+    expect(fs.readFileSync(path.join(targetDir, "CLAUDE.md"), "utf-8")).toBe(damaged);
+    expect(res.status).toBe(201);
+    const body = await res.json();
+    expect(body.applied).toEqual([]);
+    expect(body.notes).toEqual([expect.stringMatching(/^guidance_block_markers_damaged: .*CLAUDE\.md: guidance-pkg has a BEGIN or END marker without its pair/)]);
+    expect(body.verification.passed).toBe(true);
+  });
+
   // --- Test 8: POST /install mixed policy: skills approved, guidance rejected ---
   it("POST /api/packages/install mixed policy → 201 with applied + policyRejected", async () => {
     writePkg(pkgDir, MIXED_MANIFEST_YAML, {