Merge commit 'ac30fbd' into HEAD

* fix(desktop): read JSON with deeply nested overwritten values

* fix(desktop): bound exported JSON construction by view depth

* fix(desktop): preserve deep JSON numeric facts within bounded memory

---------

Co-authored-by: morluto <[email protected]>

docs/desktop-application-export.md

@@ -310,8 +310,8 @@ entry it does not read. The module reads the central directory itself, as REA
 does, and shows `zipfile` only the records it lists, reading each entry in
 bounded chunks no further than a byte past its declared size. A JSON file
 holding a number JavaScript cannot read exactly, such as an integer above 2^53,
-or nested more than 500 levels deep, gets an `error` instead of a view, as in
-REA, while text that is not one JSON
+or whose retained value nests more than 500 levels deep, gets an `error` instead of a view, as in
+REA. Duplicate keys keep their last value before the depth check. Text that is not one JSON
 document, such as JSON Lines, stays text. Format detection follows REA's
 rules. Files larger than 64 MiB get an `error` instead of a view
 and are not read. XML is read with Python's `expat` twice: with namespace

docs/mcp-contracts.md

@@ -2001,6 +2001,7 @@ bundle import/export; it does not include those view and settings tools.
 | Web investigation                                 | `browser,pcap,session,javascript-runtime`                 | page, bundle and session inspection, packet captures, JS runtime observation, evidence workflow                                                              |
 | Android application analysis                      | `android,adb,apktool,session`                             | class and method inspection, device bridge, resource decoding; add `frida` for dynamic instrumentation, `jeb` for JEB projects, `flutter` for Flutter builds |
 | Native macOS or iOS binary                        | `native,artifact,session`                                 | Mach-O, signature and property-list inspection plus container extraction                                                                                     |
+| Native analysis of a known function               | `session,enhanced,application`                            | open a binary, analyze a known function, page retained pseudocode, and export Evidence; add `direct` for focused procedure search or assembly                |
 | Managed .NET assembly                             | `managed,session`                                         | managed member comparison and reconstruction against the evidence workflow                                                                                   |
 | Electron or browser-hosted JavaScript application | `browser,electron,application,javascript-runtime,session` | runtime targets, live page inspection, bundle and capture tools, feature tracing, JavaScript semantics and reconstruction obligations                        |
 | Evidence bookkeeping only                         | `session`                                                 | open and close binaries, bundles, comparisons, unknown tracking                                                                                              |

docs/native-investigation.md

@@ -1245,6 +1245,11 @@ and slice commitments establish the same canonical entry. The result reports
 remain separate dimensions. Equal numeric addresses without applicable coordinate
 commitments do not establish same-entry correspondence. Inspect the retained
 source Evidence and coverage when correspondence remains ambiguous.
+When both inputs authenticate to the same Evidence ID and an applicable entry
+comparison is unavailable, the match reports `method: "same-evidence"`.
+This identifies one selected observation, not a correspondence between distinct
+records or proof of complete analysis. Unavailable facets and unestablished
+call coverage remain unknown.
 To aggregate already-retained comparison results, pass their exact IDs to
 `find_changed_behavior`, for example:
 

src/cli/binaryDiagnosticsCommands.ts

@@ -266,12 +266,10 @@ export const registerBinaryDiagnosticsCommands = (
       // "0x10" or "1e2".
       blockSize: cliDecimalField(
         inspectByteEntropyInputSchema.shape.block_size,
-      ).describe(
-        "Power-of-two block size from 256 to 65536 bytes (default 4096)",
-      ),
+      ).describe("Power-of-two block size from 256 to 65536 bytes"),
       offset: cliDecimalField(
         inspectByteEntropyInputSchema.shape.offset,
-      ).describe("Window start as a decimal file byte offset (default 0)"),
+      ).describe("Window start as a decimal file byte offset"),
       length: cliDecimalField(
         inspectByteEntropyInputSchema.shape.length,
       ).describe("Window length in bytes; omit to extend through EOF"),
@@ -429,16 +427,16 @@ export const registerBinaryDiagnosticsCommands = (
     options: z.object({
       maxFileBytes: cliDecimalField(
         inspectDevicetreeInputSchema.shape.max_file_bytes,
-      ).describe("Maximum FDT file size in bytes (default 4194304)"),
+      ).describe("Maximum FDT file size in bytes"),
       maxNodes: cliDecimalField(
         inspectDevicetreeInputSchema.shape.max_nodes,
-      ).describe("Maximum number of device-tree nodes (default 8192)"),
+      ).describe("Maximum number of device-tree nodes"),
       maxProperties: cliDecimalField(
         inspectDevicetreeInputSchema.shape.max_properties,
-      ).describe("Maximum number of device-tree properties (default 32768)"),
+      ).describe("Maximum number of device-tree properties"),
       maxDepth: cliDecimalField(
         inspectDevicetreeInputSchema.shape.max_depth,
-      ).describe("Maximum device-tree nesting depth (default 64)"),
+      ).describe("Maximum device-tree nesting depth"),
       ...analysisEvidenceDeliveryOptions,
     }),
     run: ({ args, options }) =>

src/cliJsonPaths.test.ts

@@ -123,7 +123,7 @@ describe("CLI JSON path normalization", () => {
       expect.objectContaining({
         path: ["executable_path"],
         code: "invalid_format",
-        message: expect.stringContaining("absolute local filesystem path"),
+        format: "regex",
       }),
     ]);
   });

src/contracts/sessionToolContracts.ts

@@ -123,7 +123,7 @@ export const SESSION_TOOL_CONTRACTS = [
   ),
   session(
     "compare_functions",
-    "Compare two explicit analyze_function Evidence records or exact retained session references across identity, exact provider text, calls, references, strings, and address-normalized CFG topology. Authenticated same-artifact entry coordinates establish correspondence independently of renamed labels; metadata and text changes remain separate. Missing or provider-incompatible facets remain truncated or unknown; every conclusion cites both Evidence sets.",
+    "Compare two explicit analyze_function Evidence records or exact retained session references across identity, exact provider text, calls, references, strings, and address-normalized CFG topology. The same authenticated Evidence record or compatible same-artifact entry coordinates establish correspondence independently of symbol origin; metadata and text changes remain separate. Missing or provider-incompatible facets remain truncated or unknown; every conclusion cites both Evidence sets.",
     functionComparisonInputSchema,
   ),
   session(

src/domain/captures/packetCapture.ts

@@ -51,7 +51,7 @@ const captureInputShape = z.strictObject({
     .int()
     .nonnegative()
     .default(0)
-    .describe("Skip this many matching packets after filtering; default 0"),
+    .describe("Skip this many matching packets after filtering"),
   match_limit: z
     .number()
     .int()

src/domain/captures/packetFields.ts

@@ -5,9 +5,7 @@ export const inspectPacketFieldsInputSchema = z.strictObject({
   kind: z
     .enum(["protocols", "fields"])
     .default("protocols")
-    .describe(
-      "Return protocol registrations or field definitions; defaults to protocols",
-    ),
+    .describe("Return protocol registrations or field definitions"),
   protocol: z
     .string()
     .min(1)
@@ -30,7 +28,7 @@ export const inspectPacketFieldsInputSchema = z.strictObject({
     .nonnegative()
     .max(Number.MAX_SAFE_INTEGER)
     .default(0)
-    .describe("Number of matching records to skip; defaults to 0"),
+    .describe("Number of matching records to skip"),
   limit: z
     .number()
     .int()

src/domain/comparisonEvidenceResult.test.ts

@@ -0,0 +1,108 @@
+import { describe, expect, it } from "vitest";
+
+import { readComparisonResult } from "./comparisonEvidenceResult.js";
+import type { Evidence } from "./evidence.js";
+import {
+  functionComparisonDimensionNameSchema,
+  functionComparisonResultSchema,
+} from "./functionComparisonSchemas.js";
+
+const source = `ev_${"a".repeat(64)}`;
+const hash = "b".repeat(64);
+const other = "c".repeat(64);
+
+const evidence = (result: unknown): Evidence =>
+  ({
+    evidence_id: `ev_${"d".repeat(64)}`,
+    evidence_links: [source],
+    parameters: { left_evidence_id: source, right_evidence_id: source },
+    normalized_result: result,
+  }) as unknown as Evidence;
+
+const baseline = () => ({
+  status: "unchanged" as const,
+  function_match: {
+    status: "matched" as const,
+    method: "same-evidence" as const,
+    left_name: "main",
+    right_name: "main",
+  },
+  left_subject_sha256: hash,
+  right_subject_sha256: hash,
+  summary: { unchanged: 8, changed: 0, unknown: 0 },
+  dimensions: functionComparisonDimensionNameSchema.options.map(
+    (dimension) => ({
+      dimension,
+      left_count: 1,
+      right_count: 1,
+      evidence_links: [source, source],
+      limitations: [],
+      status: "unchanged" as const,
+      left_digest: hash,
+      right_digest: hash,
+      text_delta: null,
+      conclusion_kind: "derived_relationship" as const,
+    }),
+  ),
+  changes: [],
+  limitations: [],
+});
+
+describe("same-evidence comparison admission", () => {
+  it("accepts a consistent complete comparison", () => {
+    const result = baseline();
+    expect(functionComparisonResultSchema.safeParse(result).success).toBe(true);
+    expect(readComparisonResult(evidence(result), "compare_functions").ok).toBe(
+      true,
+    );
+  });
+
+  it("rejects a changed dimension for one source", () => {
+    const result = baseline();
+    const changed = {
+      ...result.dimensions[0]!,
+      status: "changed" as const,
+      right_digest: other,
+    };
+    const candidate = {
+      ...result,
+      status: "changed" as const,
+      summary: { unchanged: 7, changed: 1, unknown: 0 },
+      dimensions: [changed, ...result.dimensions.slice(1)],
+      changes: [changed],
+    };
+    expect(functionComparisonResultSchema.safeParse(candidate).success).toBe(
+      true,
+    );
+    expect(
+      readComparisonResult(evidence(candidate), "compare_functions").ok,
+    ).toBe(false);
+  });
+
+  it("rejects unequal subject hashes for one source", () => {
+    const candidate = { ...baseline(), right_subject_sha256: other };
+    expect(functionComparisonResultSchema.safeParse(candidate).success).toBe(
+      true,
+    );
+    expect(
+      readComparisonResult(evidence(candidate), "compare_functions").ok,
+    ).toBe(false);
+  });
+
+  it("rejects unequal unchanged digests for one source", () => {
+    const result = baseline();
+    const candidate = {
+      ...result,
+      dimensions: [
+        { ...result.dimensions[0]!, right_digest: other },
+        ...result.dimensions.slice(1),
+      ],
+    };
+    expect(functionComparisonResultSchema.safeParse(candidate).success).toBe(
+      true,
+    );
+    expect(
+      readComparisonResult(evidence(candidate), "compare_functions").ok,
+    ).toBe(false);
+  });
+});

src/domain/comparisonEvidenceResult.ts

@@ -15,6 +15,7 @@ import {
   type ProcessCaptureComparison,
 } from "./process/processComparison.js";
 import { err, ok, type Result } from "./result.js";
+import { comparisonSourceEvidenceSides } from "./comparisonSourceEvidence.js";
 
 type ComparisonResults = {
   readonly compare_artifacts: ArtifactComparisonResult;
@@ -58,6 +59,39 @@ export function readComparisonResult(
       evidence.normalized_result,
     );
     if (!parsed.ok) return parsed;
+    if (parsed.value.function_match.method === "same-evidence") {
+      try {
+        const { left, right } = comparisonSourceEvidenceSides(evidence);
+        const sourceId = left[0];
+        const sameSource =
+          left.length === 1 &&
+          right.length === 1 &&
+          sourceId === right[0] &&
+          sourceId !== undefined &&
+          evidence.evidence_links.includes(sourceId) &&
+          parsed.value.dimensions.every(({ evidence_links }) =>
+            evidence_links.every((id) => id === sourceId),
+          );
+        const impossibleChange =
+          parsed.value.left_subject_sha256 !==
+            parsed.value.right_subject_sha256 ||
+          parsed.value.dimensions.some(
+            (dimension) =>
+              dimension.status === "changed" ||
+              (dimension.status === "unchanged" &&
+                dimension.left_digest !== dimension.right_digest),
+          );
+        if (!sameSource || impossibleChange)
+          return err(
+            new EvidenceIntegrityError(
+              "Same-Evidence function comparison must cite the same source on both sides",
+            ),
+          );
+      } catch (cause) {
+        if (cause instanceof EvidenceIntegrityError) return err(cause);
+        throw cause;
+      }
+    }
     const links = validateFindingLinks(
       evidence,
       parsed.value.dimensions.flatMap(({ evidence_links }) => evidence_links),

src/domain/desktop/appExportPython.ts

@@ -1,3 +1,4 @@
+import { PYTHON_JSON_READER } from "./appExportPythonJson.js";
 import { PYTHON_XML_READER } from "./appExportPythonXml.js";
 import { PYTHON_ZIP_HELPERS } from "./appExportPythonZip.js";
 
@@ -12,6 +13,7 @@ export const PYTHON_READY_CHECK = `
 
 export const PYTHON_IMPORTS = `from __future__ import annotations
 
+from array import array
 import contextlib
 import copy
 import hashlib
@@ -57,11 +59,6 @@ MAX_PARSED_BYTES = 4 * 1024 * 1024
 PARSED_TOO_LARGE = "larger than the 4 MiB limit for JSON and key file views"
 MAX_JSON_VIEW_DEPTH = 500
 JSON_TOO_DEEP = f"nested deeper than the {MAX_JSON_VIEW_DEPTH} levels a JSON view keeps"
-#: A JSON token after any whitespace, by group: an opening, a closing, a comma, a colon, a string's quote, or a number
-#: or literal. Strings are read by json's scanner, since a pattern repeating per escape holds memory for each.
-JSON_TOKEN = re.compile(r'[ \t\n\r]*(?:([\[{])|([\]}])|(,)|(:)|(")|(-?(?:0|[1-9][0-9]*)(?:\.[0-9]+)?(?:[eE][+-]?[0-9]+)?'
-                        r"|true|false|null))")
-JSON_SPACE = re.compile(r"[ \t\n\r]*")
 
 
 def _respelled(text: str, home: Path) -> str:
@@ -254,143 +251,7 @@ def _keyfile(text: str) -> dict:
 
 ${PYTHON_XML_READER}
 
-def _not_json(constant: str):
-    raise ValueError(f"{constant} is not JSON")
-
-
-class _Inexact(Exception):
-    """A JSON number that REA's state view refuses, since reading it would change it."""
-
-
-def _digits(text: str) -> str:
-    return re.split(r"[eE]", text.lstrip("-"))[0].replace(".", "").strip("0") or "0"
-
-
-def _js_string(value: float) -> str:
-    """How JavaScript's String() writes a finite double: an integer below 1e21 in full, any other in shortest form."""
-    return str(int(value)) if value.is_integer() and abs(value) < 1e21 else repr(value)
-
-
-def _safe_number(text: str) -> bool:
-    """lossless-json's isSafeNumber: an integer spelling within 2^53, or a float spelling that keeps its digits."""
-    if re.fullmatch(r"-?[0-9]+", text):
-        return len(text.lstrip("-")) <= 16 and abs(int(text)) <= MAX_SAFE_INTEGER
-    value = float(text)
-    if not math.isfinite(value):
-        return False
-    written = _js_string(value)
-    return written == text or _digits(written) == _digits(text)
-
-
-def _exact_number(text: str):
-    """A JSON number read only when reading it changes nothing, as REA's state view rules: its spelling and its
-    written-back form both safe, and not -0."""
-    value = float(text)
-    if (not _safe_number(text) or not math.isfinite(value) or not _safe_number(_js_string(value))
-            or (value == 0 and math.copysign(1, value) < 0)):
-        raise _Inexact(text)
-    return int(text) if re.fullmatch(r"-?[0-9]+", text) else value
-
-
-_INEXACT = object()
-_LEVEL_END = object()
-
-
-def _number_or_mark(spelling: str):
-    """A JSON number read exactly, or a mark for one REA's state view refuses."""
-    try:
-        return _exact_number(spelling)
-    except _Inexact:
-        return _INEXACT
-
-
-def _holds_inexact(value) -> bool:
-    """Whether a parsed JSON value still holds a marked number once duplicate keys kept their last value; one
-    iterator per nesting level, so no child list is copied."""
-    levels = [iter((value,))]
-    while levels:
-        item = next(levels[-1], _LEVEL_END)
-        if item is _LEVEL_END:
-            levels.pop()
-        elif item is _INEXACT:
-            return True
-        elif isinstance(item, dict):
-            levels.append(iter(item.values()))
-        elif isinstance(item, list):
-            levels.append(iter(item))
-    return False
-
-
-def _deeper_than(root, limit: int) -> bool:
-    """Whether a parsed JSON value nests deeper than a limit, as REA checks it: a value's depth is the number of
-    iterators open above it, one per nesting level, so no child list is copied."""
-    levels = [iter((root,))]
-    while levels:
-        item = next(levels[-1], _LEVEL_END)
-        if item is _LEVEL_END:
-            levels.pop()
-        elif len(levels) - 1 > limit:
-            return True
-        elif isinstance(item, dict):
-            levels.append(iter(item.values()))
-        elif isinstance(item, list):
-            levels.append(iter(item))
-    return False
-
-
-def _is_json(text: str) -> bool:
-    """Whether text is one JSON value as REA's state view reads it, checked a token at a time without building it or
-    recursing: it holds a byte per open container and one string at a time, so text too deep for Python's parser or
-    too large to parse into a view is still told apart from other text."""
-    containers, expect, empty, at = bytearray(), "value", False, 0
-    while True:
-        token = JSON_TOKEN.match(text, at)
-        if token is None:
-            break
-        kind, at = token.lastindex, token.end()
-        if kind == 5:
-            try:
-                at = json.decoder.scanstring(text, at)[1]
-            except ValueError:
-                return False
-        if kind == 1 and expect == "value":
-            containers.append(ord(text[at - 1]))
-            expect, empty = ("value" if text[at - 1] == "[" else "key"), True
-        # A closing bracket's code is its opening's plus two.
-        elif kind == 2 and (expect == "after" or empty) and containers and containers[-1] == ord(text[at - 1]) - 2:
-            containers.pop()
-            expect, empty = "after", False
-        elif kind == 3 and expect == "after" and containers:
-            expect = "value" if containers[-1] == ord("[") else "key"
-        elif kind == 4 and expect == "colon":
-            expect = "value"
-        elif kind >= 5 and (expect == "value" or (kind == 5 and expect == "key")):
-            expect, empty = ("colon" if expect == "key" else "after"), False
-        else:
-            return False
-    return expect == "after" and not containers and JSON_SPACE.fullmatch(text, at) is not None
-
-
-def _json_view(text: str, size: int):
-    """A JSON text's format and view, or why it has none, as REA reads it; None when it is not JSON. Text over the
-    parsed-view limit, or nested past Python's recursion limit, is told apart without building its value."""
-    if size > MAX_PARSED_BYTES:
-        return {"format": "json", "view": None, "error": PARSED_TOO_LARGE} if _is_json(text) else None
-    # The whole text must parse, and duplicate keys settle, before an inexact number makes it JSON with an error.
-    try:
-        view = json.loads(text, parse_constant=_not_json, parse_float=_number_or_mark, parse_int=_number_or_mark)
-    except RecursionError:
-        # Nesting too deep for Python to parse is far deeper than REA's view keeps, once the rest of it is JSON too.
-        return {"format": "json", "view": None, "error": JSON_TOO_DEEP} if _is_json(text) else None
-    except ValueError:
-        return None
-    if _holds_inexact(view):
-        return {"format": "json", "view": None,
-                "error": "a number in it cannot be read exactly, such as an integer above 2^53"}
-    if _deeper_than(view, MAX_JSON_VIEW_DEPTH):
-        return {"format": "json", "view": None, "error": JSON_TOO_DEEP}
-    return {"format": "json", "view": view, "truncated": False}
-
+${PYTHON_JSON_READER}
 
 def _text_view(name: str, text: str, size: int) -> dict:
     """The format REA's state view detects for decoded text of size bytes, and its view; a JSON or key file over the

src/domain/desktop/appExportPythonJson.ts

@@ -0,0 +1,231 @@
+/** JSON parsing and bounded retained-view checks for exported desktop environments. */
+export const PYTHON_JSON_READER = String.raw`
+#: A JSON token after any whitespace, by group: an opening, a closing, a comma, a colon, a string's quote, or a number
+#: or literal. Strings are read by json's scanner, since a pattern repeating per escape holds memory for each.
+JSON_TOKEN = re.compile(r'[ \t\n\r]*(?:([\[{])|([\]}])|(,)|(:)|(")|(-?(?:0|[1-9][0-9]*)(?:\.[0-9]+)?(?:[eE][+-]?[0-9]+)?'
+                        r"|true|false|null))")
+JSON_SPACE = re.compile(r"[ \t\n\r]*")
+
+
+class _Inexact(Exception):
+    """A JSON number that REA's state view refuses, since reading it would change it."""
+
+
+def _digits(text: str) -> str:
+    return re.split(r"[eE]", text.lstrip("-"))[0].replace(".", "").strip("0") or "0"
+
+
+def _js_string(value: float) -> str:
+    """How JavaScript's String() writes a finite double: an integer below 1e21 in full, any other in shortest form."""
+    return str(int(value)) if value.is_integer() and abs(value) < 1e21 else repr(value)
+
+
+def _safe_number(text: str) -> bool:
+    """lossless-json's isSafeNumber: an integer spelling within 2^53, or a float spelling that keeps its digits."""
+    if re.fullmatch(r"-?[0-9]+", text):
+        return len(text.lstrip("-")) <= 16 and abs(int(text)) <= MAX_SAFE_INTEGER
+    value = float(text)
+    if not math.isfinite(value):
+        return False
+    written = _js_string(value)
+    return written == text or _digits(written) == _digits(text)
+
+
+def _exact_number(text: str):
+    """A JSON number read only when reading it changes nothing, as REA's state view rules: its spelling and its
+    written-back form both safe, and not -0."""
+    value = float(text)
+    if (not _safe_number(text) or not math.isfinite(value) or not _safe_number(_js_string(value))
+            or (value == 0 and math.copysign(1, value) < 0)):
+        raise _Inexact(text)
+    return int(text) if re.fullmatch(r"-?[0-9]+", text) else value
+
+
+_INEXACT = object()
+_DEEP = object()
+_DEEP_INEXACT = object()
+_LEVEL_END = object()
+_INVALID_JSON = object()
+JSON_ATOMS = {"true": True, "false": False, "null": None}
+
+
+def _number_or_mark(spelling: str):
+    """A JSON number read exactly, or a mark for one REA's state view refuses."""
+    try:
+        return _exact_number(spelling)
+    except _Inexact:
+        return _INEXACT
+
+
+def _holds_inexact(value) -> bool:
+    """Whether a parsed JSON value still holds a marked number once duplicate keys kept their last value; one
+    iterator per nesting level, so no child list is copied."""
+    levels = [iter((value,))]
+    while levels:
+        item = next(levels[-1], _LEVEL_END)
+        if item is _LEVEL_END:
+            levels.pop()
+        elif item is _INEXACT or item is _DEEP_INEXACT:
+            return True
+        elif isinstance(item, dict):
+            levels.append(iter(item.values()))
+        elif isinstance(item, list):
+            levels.append(iter(item))
+    return False
+
+
+def _deeper_than(root, limit: int) -> bool:
+    """Whether a parsed JSON value nests deeper than a limit, as REA checks it: a value's depth is the number of
+    iterators open above it, one per nesting level, so no child list is copied."""
+    levels = [iter((root,))]
+    while levels:
+        item = next(levels[-1], _LEVEL_END)
+        if item is _LEVEL_END:
+            levels.pop()
+        elif item is _DEEP or item is _DEEP_INEXACT:
+            return True
+        elif len(levels) - 1 > limit:
+            return True
+        elif isinstance(item, dict):
+            levels.append(iter(item.values()))
+        elif isinstance(item, list):
+            levels.append(iter(item))
+    return False
+
+
+def _read_json(text: str, build: bool = True):
+    """One JSON value, or _INVALID_JSON, read without recursion so duplicate keys settle before depth is checked.
+    Deep containers are summarized rather than built; exact-number marks still follow last-key-wins semantics.
+    With build=False, only syntax is checked: one byte per open container and one decoded string at a time."""
+    containers, expect, empty, at = bytearray(), "value", False, 0
+    values, keys, root = [], [], _INVALID_JSON
+    deep_bad, deep_key_at, bad_keys = bytearray(), array("I"), {}
+
+    def keep(value) -> None:
+        nonlocal root
+        if not values:
+            root = value
+        elif containers[-1] == ord("["):
+            values[-1].append(value)
+        else:
+            values[-1][keys[-1]] = value
+
+    def record_deep(bad: bool) -> None:
+        """Summarize a finished child; keep only object keys with live inexact values."""
+        depth = len(deep_bad) - 1
+        if containers[-1] == ord("["):
+            deep_bad[-1] |= 2 | bad
+            return
+        marked = bad_keys.get(depth)
+        if bad or marked is not None:
+            key, _ = json.decoder.scanstring(text, deep_key_at[-1])
+            if bad:
+                if marked is None:
+                    marked = key
+                elif isinstance(marked, str):
+                    if marked != key:
+                        marked = {marked, key}
+                else:
+                    marked.add(key)
+            else:
+                if isinstance(marked, str):
+                    if marked == key:
+                        marked = None
+                else:
+                    marked.discard(key)
+                    if len(marked) == 1:
+                        marked = next(iter(marked))
+            if marked is None:
+                bad_keys.pop(depth, None)
+            else:
+                bad_keys[depth] = marked
+            deep_bad[-1] = 2 | (marked is not None)
+        else:
+            deep_bad[-1] |= 2
+
+    while True:
+        token = JSON_TOKEN.match(text, at)
+        if token is None:
+            break
+        kind, at = token.lastindex, token.end()
+        if kind == 5:
+            string_at = at
+            try:
+                value, at = json.decoder.scanstring(text, at)
+            except ValueError:
+                return _INVALID_JSON
+        if kind == 1 and expect == "value":
+            if build:
+                if deep_bad or len(containers) >= MAX_JSON_VIEW_DEPTH:
+                    deep_bad.append(0)
+                    deep_key_at.append(0)
+                else:
+                    value = [] if text[at - 1] == "[" else {}
+                    keep(value)
+                    values.append(value)
+                    keys.append(None)
+            containers.append(ord(text[at - 1]))
+            expect, empty = ("value" if text[at - 1] == "[" else "key"), True
+        # A closing bracket's code is its opening's plus two.
+        elif kind == 2 and (expect == "after" or empty) and containers and containers[-1] == ord(text[at - 1]) - 2:
+            opening = containers.pop()
+            if build:
+                if deep_bad:
+                    state = deep_bad.pop()
+                    bad = bool(state & 1)
+                    deep_key_at.pop()
+                    bad_keys.pop(len(deep_bad), None)
+                    if deep_bad:
+                        record_deep(bad)
+                    else:
+                        keep((_DEEP_INEXACT if bad else _DEEP) if state & 2 else ([] if opening == ord("[") else {}))
+                else:
+                    values.pop()
+                    keys.pop()
+            expect, empty = "after", False
+        elif kind == 3 and expect == "after" and containers:
+            expect = "value" if containers[-1] == ord("[") else "key"
+        elif kind == 4 and expect == "colon":
+            expect = "value"
+        elif kind >= 5 and (expect == "value" or (kind == 5 and expect == "key")):
+            if build:
+                if expect == "key":
+                    if deep_bad:
+                        deep_key_at[-1] = string_at
+                    else:
+                        keys[-1] = value
+                else:
+                    if kind == 6:
+                        value = JSON_ATOMS.get(token[6], _INVALID_JSON)
+                        if value is _INVALID_JSON:
+                            value = _number_or_mark(token[6])
+                    if deep_bad:
+                        record_deep(value is _INEXACT)
+                    else:
+                        keep(value)
+            expect, empty = ("colon" if expect == "key" else "after"), False
+        else:
+            return _INVALID_JSON
+    if expect != "after" or containers or JSON_SPACE.fullmatch(text, at) is None:
+        return _INVALID_JSON
+    return root if build else True
+
+
+def _json_view(text: str, size: int):
+    """A JSON text's format and view, or why it has none, as REA reads it; None when it is not JSON. Text over the
+    parsed-view limit is told apart without building its value."""
+    if size > MAX_PARSED_BYTES:
+        valid = _read_json(text, build=False) is not _INVALID_JSON
+        return {"format": "json", "view": None, "error": PARSED_TOO_LARGE} if valid else None
+    # The whole text must parse, and duplicate keys settle, before an inexact number makes it JSON with an error.
+    view = _read_json(text)
+    if view is _INVALID_JSON:
+        return None
+    if _holds_inexact(view):
+        return {"format": "json", "view": None,
+                "error": "a number in it cannot be read exactly, such as an integer above 2^53"}
+    if _deeper_than(view, MAX_JSON_VIEW_DEPTH):
+        return {"format": "json", "view": None, "error": JSON_TOO_DEEP}
+    return {"format": "json", "view": view, "truncated": False}
+
+`;

src/domain/functionComparison.ts

@@ -26,7 +26,8 @@ export const compareFunctions = (
   const dimensions = compareDimensions(left, right, {
     links,
     providersDiffer,
-    sameEntry: match.method === "same-entry",
+    sameIdentity:
+      match.method === "same-entry" || match.method === "same-evidence",
     coordinateContext,
   });
   const changes = dimensions.filter(({ status }) => status !== "unchanged");

src/domain/functionComparisonDimensions.ts

@@ -34,7 +34,7 @@ type ComparisonContext = Pick<
   DimensionResultInput,
   "links" | "providersDiffer"
 > & {
-  readonly sameEntry: boolean;
+  readonly sameIdentity: boolean;
   readonly coordinateContext: FunctionSnapshotCoordinateContext;
 };
 
@@ -554,7 +554,7 @@ const compareIdentity = (
   context: ComparisonContext,
 ): FunctionDimension => {
   if (
-    !context.sameEntry &&
+    !context.sameIdentity &&
     (!hasStableNativeSymbol(
       left.dossier.procedure.name,
       left.dossier.procedure.symbol,

src/domain/functionComparisonNormalization.ts

@@ -49,13 +49,21 @@ export const functionMatch = (
             left_name: leftName,
             right_name: rightName,
           };
+  }
+  if (left.evidence.evidence_id === right.evidence.evidence_id)
+    return {
+      status: "matched",
+      method: "same-evidence",
+      left_name: leftName,
+      right_name: rightName,
+    };
+  if (coordinateContext === "common")
     return {
       status: "ambiguous",
       method: "explicit",
       left_name: leftName,
       right_name: rightName,
     };
-  }
   const stableNames =
     hasStableNativeSymbol(leftName, left.dossier.procedure.symbol) &&
     hasStableNativeSymbol(rightName, right.dossier.procedure.symbol);

src/domain/functionComparisonSchemas.ts

@@ -79,6 +79,12 @@ const functionMatchSchema = z.union([
     left_name: z.string(),
     right_name: z.string(),
   }),
+  z.object({
+    status: z.literal("matched"),
+    method: z.literal("same-evidence"),
+    left_name: z.string(),
+    right_name: z.string(),
+  }),
   z.object({
     status: z.enum(["mismatched", "ambiguous"]),
     method: z.literal("explicit"),

src/domain/localPath.test.ts

@@ -21,11 +21,20 @@ const PATHS = [
 ];
 
 it("matches the host path module for absolute local paths", () => {
+  const checked: string[] = [];
   for (const path of PATHS) {
+    checked.push(path);
     expect(absoluteLocalPathStringSchema.safeParse(path).success).toBe(
       isAbsolute(path),
     );
   }
+  expect(checked).toEqual(
+    expect.arrayContaining([
+      "/absolute/path",
+      "relative/path",
+      "file:///absolute/path",
+    ]),
+  );
   expect(absoluteLocalPathStringSchema.safeParse("").success).toBe(false);
   expect(
     absoluteLocalPathStringSchema.safeParse("/absolute/with\0nul").success,
@@ -40,8 +49,18 @@ it("keeps the Windows absolute-path pattern valid in every client mode", () => {
       () => new RegExp(windowsAbsolutePathPattern.source, flags),
       flags,
     ).not.toThrow();
-  for (const path of PATHS)
+  const checked: string[] = [];
+  for (const path of PATHS) {
+    checked.push(path);
     expect(windowsAbsolutePathPattern.test(path), path).toBe(
       win32.isAbsolute(path),
     );
+  }
+  expect(checked).toEqual(
+    expect.arrayContaining([
+      "C:\\absolute\\path",
+      "C:relative/path",
+      "/absolute/path",
+    ]),
+  );
 });

src/domain/signals/signalDecoders.ts

@@ -24,9 +24,7 @@ export const inspectSignalDecodersInputSchema = z.strictObject({
     .nonnegative()
     .max(Number.MAX_SAFE_INTEGER)
     .default(0)
-    .describe(
-      "Number of matching decoders or help lines to skip; defaults to 0",
-    ),
+    .describe("Number of matching decoders or help lines to skip"),
   limit: z
     .number()
     .int()

src/domain/signals/signalRecording.ts

@@ -31,7 +31,7 @@ const signalInputShape = z.strictObject({
     .int()
     .nonnegative()
     .default(0)
-    .describe("Skip this many literal LF-separated output lines; default 0"),
+    .describe("Skip this many literal LF-separated output lines"),
   line_limit: z
     .number()
     .int()

src/native/pe/PeCertificateParser.test.ts

@@ -105,6 +105,21 @@ it("reports unsigned attribute OIDs and incomplete nested coverage", () => {
   }
 });
 
+it.each([false, true])(
+  "rejects a misaligned certificate table (PE32+ = %s)",
+  (plus) => {
+    const aligned = peCertificateFixture(plus, undefined, undefined, true);
+    expect(parse(aligned).coverage.status).toBe("complete");
+    const shifted = Buffer.concat([
+      aligned.subarray(0, 0x200),
+      Buffer.alloc(1),
+      aligned.subarray(0x200),
+    ]);
+    shifted.writeUInt32LE(0x201, 0x98 + (plus ? 112 : 96) + 4 * 8);
+    expect(() => parse(shifted)).toThrow(/certificate table offset.*aligned/u);
+  },
+);
+
 it("accepts only zero eight-byte alignment padding included in dwLength", () => {
   for (const plus of [false, true]) {
     const bytes = peCertificateFixture(plus, undefined, undefined, true);

src/native/pe/PeCertificateParser.ts

@@ -79,6 +79,8 @@ export const parsePeCertificates = (
   const directoryAt = optionalHeaderOffset + security.offset;
   if (tableSize === 0 || tableOffset < headerSize)
     fail("PE certificate table offset overlaps headers or has zero size.");
+  if (tableOffset % 8 !== 0)
+    fail("PE certificate table offset must be aligned to eight bytes.");
   requireRange(bytes, tableOffset, tableSize);
   const table = bytes.subarray(tableOffset, tableOffset + tableSize);
   const entries: PeCertificates["entries"] = [];

tests/acceptance/applications/electronInvalidPaths.test.ts

@@ -255,11 +255,11 @@ cliTest(
       code: "invalid_request",
       details: {
         issues: [
-          {
+          expect.objectContaining({
             path: ["executable_path"],
             reason: "invalid_format",
-            message: expect.stringContaining("absolute local filesystem path"),
-          },
+            expected: "regex",
+          }),
         ],
       },
     });

tests/acceptance/tools/localToolContracts.test.ts

@@ -4,6 +4,7 @@ import { join } from "node:path";
 import { fileURLToPath } from "node:url";
 import { promisify } from "node:util";
 import { expect, it } from "vitest";
+import { z } from "zod";
 
 import { toolContract } from "../../../src/contracts/toolContracts.js";
 import { createEvidence, parseEvidence } from "../../../src/domain/evidence.js";
@@ -329,21 +330,84 @@ const pathRequests: readonly [string, Record<string, unknown>][] = [
   ["start_gdb_session", { inferior_tty: nul }],
 ];
 
+const nulIssuePaths = (
+  value: unknown,
+  path: readonly (string | number)[] = [],
+): (string | number)[][] => {
+  if (typeof value === "string") return value.includes("\0") ? [[...path]] : [];
+  if (Array.isArray(value))
+    return value.flatMap((item, index) =>
+      nulIssuePaths(item, [...path, index]),
+    );
+  if (typeof value === "object" && value !== null)
+    return Object.entries(value).flatMap(([key, item]) =>
+      nulIssuePaths(item, [...path, key]),
+    );
+  return [];
+};
+
 it("rejects OS-invalid local inputs through the real advertised MCP contracts", async () => {
   const { call } = await connectLocalToolsMcp();
+  const checked: string[] = [];
   for (const [name, arguments_] of pathRequests) {
-    const response = await call(name, arguments_);
-    expect(response.isError, name).toBe(true);
-    expect(JSON.stringify(response.content), name).toContain("NUL");
+    const paths = nulIssuePaths(arguments_);
+    expect(paths.length, name).toBeGreaterThan(0);
+    const error = parseMcpToolError(await call(name, arguments_)).error;
+    expect(error, name).toMatchObject({
+      code: "invalid_request",
+      details: { operation: name },
+    });
+    const issues = z
+      .object({
+        issues: z.array(
+          z.object({
+            path: z.array(z.union([z.string(), z.number()])),
+            reason: z.string(),
+            message: z.string(),
+            expected: z.unknown().optional(),
+          }),
+        ),
+      })
+      .parse(error.details).issues;
+    expect(issues, name).toEqual(
+      expect.arrayContaining(
+        paths.map((path) =>
+          expect.objectContaining({
+            path,
+            reason: "invalid_format",
+            expected: "regex",
+            message: expect.stringMatching(/\bNUL\b|null byte|zero byte/i),
+          }),
+        ),
+      ),
+    );
+    checked.push(name);
   }
+  expect(checked).toEqual(
+    expect.arrayContaining([
+      "extract_firmware",
+      "inspect_wasm_artifact",
+      "demangle_swift",
+      "capture_electron_scenario",
+    ]),
+  );
   const relative = await call("extract_firmware", {
     path: "/tmp/firmware.bin",
     output_directory: "relative-output",
   });
-  expect(relative.isError).toBe(true);
-  expect(JSON.stringify(relative.content)).toContain(
-    "absolute local filesystem path",
-  );
+  expect(parseMcpToolError(relative).error).toMatchObject({
+    code: "invalid_request",
+    details: {
+      operation: "extract_firmware",
+      issues: [
+        expect.objectContaining({
+          path: ["output_directory"],
+          reason: "invalid_format",
+          expected: "regex",
+        }),
+      ],
+    },
+  });
 }, 60_000);
 
 const ignoredOptions = [

tests/boundary/cli/cliHelpDefaultAnnotations.test.ts

@@ -0,0 +1,87 @@
+import { describe, expect, it } from "vitest";
+
+import { createCli } from "../../../src/cli.js";
+
+type CliInstance = ReturnType<typeof createCli>;
+
+const serve = async (
+  cli: CliInstance,
+  argv: readonly string[],
+): Promise<{ readonly stdout: string; readonly exitCode: number }> => {
+  let stdout = "";
+  let exitCode = 0;
+  await cli.serve([...argv], {
+    env: {},
+    exit: (code) => {
+      exitCode = code;
+    },
+    stdout: (text) => {
+      stdout += text;
+    },
+  });
+  return { stdout, exitCode };
+};
+
+/**
+ * Options whose owning field already declares a schema default. The help
+ * renderer appends that default, so the description must not restate it.
+ */
+const singleDefaultOptions: readonly {
+  readonly command: string;
+  readonly options: readonly string[];
+}[] = [
+  { command: "inspect-byte-entropy", options: ["--block-size", "--offset"] },
+  {
+    command: "inspect-devicetree",
+    options: [
+      "--max-file-bytes",
+      "--max-nodes",
+      "--max-properties",
+      "--max-depth",
+    ],
+  },
+  {
+    command: "decode-signal-recording",
+    options: ["--line_offset", "--line_limit"],
+  },
+  {
+    command: "inspect-packet-capture",
+    options: ["--match_offset", "--match_limit"],
+  },
+  {
+    command: "inspect-packet-fields",
+    options: ["--kind", "--offset"],
+  },
+  { command: "inspect-signal-decoders", options: ["--offset"] },
+];
+
+const optionLine = (help: string, option: string): string | undefined => {
+  const line = help
+    .split(/\r?\n/u)
+    .find((candidate) => candidate.trimStart().startsWith(`${option} `));
+  return line?.trim();
+};
+
+describe("CLI help default annotations", () => {
+  it("states each schema-owned option default exactly once", async () => {
+    const cli = createCli({});
+    const repeated: string[] = [];
+    for (const { command, options } of singleDefaultOptions) {
+      const { stdout, exitCode } = await serve(cli, [command, "--help"]);
+      expect(exitCode, command).toBe(0);
+      for (const option of options) {
+        const line = optionLine(stdout, option);
+        if (line === undefined) {
+          repeated.push(`${command} ${option}: option line missing`);
+          continue;
+        }
+        const statements = line.match(/default/giu)?.length ?? 0;
+        if (statements !== 1)
+          repeated.push(
+            `${command} ${option}: ${statements} default statements`,
+          );
+      }
+    }
+    expect(repeated).toEqual([]);
+  });
+});

tests/boundary/mcp/absoluteLocalPathSchema.test.ts

@@ -13,7 +13,7 @@ interface PathInputCase {
   readonly field: string;
   readonly valid: Readonly<Record<string, unknown>>;
   readonly invalid: Readonly<Record<string, unknown>>;
-  readonly issuePath?: readonly string[];
+  readonly issuePath: readonly string[];
 }
 
 const createMcp = async (
@@ -104,7 +104,13 @@ const inputCases = (
     field: string,
     valid: Readonly<Record<string, unknown>>,
     invalid: Readonly<Record<string, unknown>>,
-  ): PathInputCase => ({ name, field, valid, invalid });
+  ): PathInputCase => ({
+    name,
+    field,
+    valid,
+    invalid,
+    issuePath: field.split("."),
+  });
 
   return [
     pathCase("open_binary", "path", { path: absolute }, { path: relative }),
@@ -246,8 +252,7 @@ it("advertises full host-absolute path constraints after SDK schema conversion",
     const ajv = new Ajv2020({ strict: false, validateFormats: false });
     const absolute = resolve("rea-absolute-input");
     const relative = "relative-input";
-
-    for (const { name, field, valid, invalid } of [
+    const schemaCases = [
       ...inputCases(absolute, relative),
       {
         name: "inspect_go_binary",
@@ -276,7 +281,9 @@ it("advertises full host-absolute path constraints after SDK schema conversion",
           right_bundle_path: absolute,
         },
       },
-    ]) {
+    ];
+    const checked: string[] = [];
+    for (const { name, field, valid, invalid } of schemaCases) {
       const schema = listed.tools.find(
         (tool) => tool.name === name,
       )?.inputSchema;
@@ -288,7 +295,16 @@ it("advertises full host-absolute path constraints after SDK schema conversion",
         validate(valid),
         `${name}.${field}: ${JSON.stringify(validate.errors)}`,
       ).toBe(true);
+      checked.push(`${name}.${field}`);
     }
+    expect(checked).toEqual(
+      expect.arrayContaining([
+        "open_binary.path",
+        "extract_firmware.output_directory",
+        "inspect_go_binary.path NUL",
+        "compare_bundles.left_bundle_path empty",
+      ]),
+    );
     expect(firmwareCalls).toEqual([]);
   } finally {
     await close();
@@ -299,19 +315,39 @@ it("rejects relative paths through in-memory MCP handlers", async () => {
   const firmwareCalls: string[] = [];
   const { client, close } = await createMcp(firmwareCalls);
   try {
-    for (const { name, field, invalid, issuePath } of inputCases(
-      resolve("rea-absolute-input"),
-      "relative-input",
-    )) {
+    const cases = inputCases(resolve("rea-absolute-input"), "relative-input");
+    const checked: string[] = [];
+    for (const { name, field, invalid, issuePath } of cases) {
       const result = await client.callTool({ name, arguments: invalid });
       expect(result.isError, `${name}.${field}`).toBe(true);
-      expect(JSON.stringify(result), `${name}.${field}`).toContain("absolute");
-      if (issuePath !== undefined)
-        expect(parseMcpToolError(result).error.details).toMatchObject({
-          operation: name,
-          issues: [{ path: issuePath, reason: "invalid_format" }],
-        });
+      expect(parseMcpToolError(result).error, `${name}.${field}`).toMatchObject(
+        {
+          code: "invalid_request",
+          details: {
+            operation: name,
+            issues: [
+              expect.objectContaining({
+                path: issuePath,
+                reason: "invalid_format",
+                expected: "regex",
+              }),
+            ],
+          },
+        },
+      );
+      checked.push(`${name}.${field}`);
     }
+    expect(checked).toEqual(
+      expect.arrayContaining([
+        "open_binary.path",
+        "open_binary.snapshot_path",
+        "extract_firmware.path",
+        "extract_firmware.output_directory",
+        "inspect_analysis_view.source.path",
+        "capture_browser_scenario.browser.executable_path",
+        "capture_electron_scenario.application_root",
+      ]),
+    );
     expect(firmwareCalls).toEqual([]);
   } finally {
     await close();

tests/boundary/mcp/ghidraEvidenceMcp.test.ts

@@ -703,9 +703,7 @@ describe("Ghidra MCP evidence parity", () => {
         },
         limitations: expect.arrayContaining([
           expect.stringContaining("default auto-analysis complete"),
-          expect.stringContaining(
-            "original executable bytes are never written",
-          ),
+          expect.stringContaining("original executable bytes are unchanged"),
         ]),
       });
       const directAnalyzed = await new EnhancedTools(session).execute(

tests/boundary/mcp/sameFunctionObservation.test.ts

@@ -0,0 +1,211 @@
+import { afterAll, expect, it } from "vitest";
+import { Ajv2020 } from "ajv/dist/2020.js";
+import type { AnySchema } from "ajv";
+import type { Client } from "@modelcontextprotocol/client";
+import { createApplicationMcpHarness } from "../../fixtures/applicationMcpHarness.js";
+import { createTestBinarySession } from "../../fixtures/binarySession.js";
+import { createMcpSchemaValidation } from "../../fixtures/mcpSchemaValidation.js";
+import { parseMcpToolError } from "../../fixtures/mcpToolError.js";
+import { FUNCTION_COMPARISON_EXAMPLE } from "../../../src/contracts/functionComparisonExample.js";
+import {
+  createEvidence,
+  parseEvidence,
+  type Evidence,
+} from "../../../src/domain/evidence.js";
+import { functionDossierSchema } from "../../../src/domain/native/functionDossier.js";
+import { functionComparisonResultSchema } from "../../../src/domain/functionComparisonSchemas.js";
+
+const example = FUNCTION_COMPARISON_EXAMPLE.left;
+const dossier = functionDossierSchema.parse(example.normalized_result);
+const { symbol: _symbol, ...procedure } = dossier.procedure;
+const observation = (request: string) =>
+  createEvidence(
+    { path: "/tmp/fixture", sha256: "0".repeat(64), format: "mach-o" },
+    example.provider,
+    {
+      operation: "analyze_function",
+      parameters: { procedure: request },
+      result: {
+        ...dossier,
+        procedure,
+        comments: [],
+        facet_availability: {
+          ...dossier.facet_availability,
+          comments: { available: false, reason: "Fixture has no comments." },
+        },
+      },
+      confidence: "derived",
+      authority: "shipped-artifact",
+      relationshipCoverage: { status: "complete" },
+    },
+  );
+const main = observation("main");
+const another = observation("another-selector");
+const schemaValidation = createMcpSchemaValidation();
+afterAll(() => schemaValidation.clear());
+const ref = (evidence_id: string) => ({
+  kind: "retained-evidence",
+  evidence_id,
+});
+
+const expectRejectedDimensionCitation = async (
+  client: Client,
+  comparison: Evidence,
+) => {
+  const original = functionComparisonResultSchema.parse(
+    comparison.normalized_result,
+  );
+  const altered = (dimension: (typeof original.dimensions)[number]) =>
+    dimension.dimension === "comments"
+      ? {
+          ...dimension,
+          evidence_links: [main.evidence_id, another.evidence_id],
+        }
+      : dimension;
+  const result = functionComparisonResultSchema.parse({
+    ...original,
+    dimensions: original.dimensions.map(altered),
+    changes: original.changes.map(altered),
+  });
+  const invalid = createEvidence(undefined, comparison.provider, {
+    predicateType: comparison.predicate_type,
+    operation: comparison.operation,
+    parameters: comparison.parameters,
+    result,
+    confidence: comparison.confidence,
+    authority: comparison.authority,
+    limitations: comparison.limitations,
+    evidenceLinks: [main.evidence_id, another.evidence_id],
+  });
+  const response = await client.callTool({
+    name: "find_changed_behavior",
+    arguments: { comparisons: [invalid] },
+  });
+  expect(response.isError).toBe(true);
+  expect(parseMcpToolError(response).error.code).toBe(
+    "evidence_integrity_mismatch",
+  );
+};
+
+it.each(["full", "compact"] as const)(
+  "compares the same authenticated observation while preserving incomplete facets (%s)",
+  async (profile) => {
+    const session = createTestBinarySession(() => {
+      throw new Error("offline comparison must not launch a provider");
+    });
+    expect(session.recordEvidence(main).ok).toBe(true);
+    expect(session.recordEvidence(another).ok).toBe(true);
+    const { client } = await createApplicationMcpHarness({
+      session,
+      schemaValidator: schemaValidation,
+      serverOptions: {
+        environment: { REA_MCP_OUTPUT_SCHEMA_PROFILE: profile },
+      },
+    });
+    const schema = (await client.listTools()).tools.find(
+      ({ name }) => name === "compare_functions",
+    )?.outputSchema;
+    if (schema === undefined) throw new Error("Missing output schema");
+    const reply = await client.callTool({
+      name: "compare_functions",
+      arguments: { left: ref(main.evidence_id), right: ref(main.evidence_id) },
+    });
+    expect(reply.isError, JSON.stringify(reply.content)).not.toBe(true);
+    expect(
+      new Ajv2020({ strict: false }).validate(
+        schema as AnySchema,
+        reply.structuredContent,
+      ),
+    ).toBe(true);
+    const result = parseEvidence(reply.structuredContent).normalized_result;
+    expect(result).toMatchObject({
+      status: "unknown",
+      function_match: { status: "matched", method: "same-evidence" },
+      dimensions: expect.arrayContaining([
+        expect.objectContaining({ dimension: "identity", status: "unchanged" }),
+        expect.objectContaining({ dimension: "comments", status: "unknown" }),
+      ]),
+    });
+    const comparison = parseEvidence(reply.structuredContent);
+    const behavior = await client.callTool({
+      name: "find_changed_behavior",
+      arguments: { comparisons: [ref(comparison.evidence_id)] },
+    });
+    expect(behavior.isError, JSON.stringify(behavior.content)).not.toBe(true);
+    const behaviorResult = parseEvidence(
+      behavior.structuredContent,
+    ).normalized_result;
+    expect(behaviorResult).toMatchObject({
+      behavior_status: "unknown",
+      findings: {
+        items: expect.arrayContaining([
+          expect.objectContaining({ dimension: "comments", status: "unknown" }),
+        ]),
+      },
+    });
+    expect(behaviorResult).toMatchObject({
+      findings: {
+        items: expect.not.arrayContaining([
+          expect.objectContaining({ dimension: "identity" }),
+        ]),
+      },
+    });
+    const contradictory = createEvidence(undefined, comparison.provider, {
+      predicateType: comparison.predicate_type,
+      operation: comparison.operation,
+      parameters: {
+        left_evidence_id: main.evidence_id,
+        right_evidence_id: another.evidence_id,
+      },
+      result: comparison.normalized_result,
+      confidence: comparison.confidence,
+      authority: comparison.authority,
+      limitations: comparison.limitations,
+      evidenceLinks: [main.evidence_id, another.evidence_id],
+    });
+    const contradictoryBehavior = await client.callTool({
+      name: "find_changed_behavior",
+      arguments: { comparisons: [contradictory] },
+    });
+    expect(contradictoryBehavior.isError).toBe(true);
+    expect(parseMcpToolError(contradictoryBehavior).error.code).toBe(
+      "evidence_integrity_mismatch",
+    );
+    await expectRejectedDimensionCitation(client, comparison);
+    const distinct = await client.callTool({
+      name: "compare_functions",
+      arguments: {
+        left: ref(main.evidence_id),
+        right: ref(another.evidence_id),
+      },
+    });
+    expect(
+      parseEvidence(distinct.structuredContent).normalized_result,
+    ).toMatchObject({
+      function_match: { status: "ambiguous" },
+    });
+    const rebound = await client.callTool({
+      name: "compare_functions",
+      arguments: {
+        left: main,
+        right: { ...main, caller_input_path: "/tmp/alternate-spelling" },
+      },
+    });
+    expect(
+      parseEvidence(rebound.structuredContent).normalized_result,
+    ).toMatchObject({
+      function_match: { status: "matched", method: "same-evidence" },
+    });
+    const tampered = await client.callTool({
+      name: "compare_functions",
+      arguments: {
+        left: ref(main.evidence_id),
+        right: { ...main, normalized_result: { ...dossier, procedure } },
+      },
+    });
+    expect(tampered.isError).toBe(true);
+    expect(parseMcpToolError(tampered).error.code).toBe(
+      "evidence_integrity_mismatch",
+    );
+  },
+);

tests/boundary/mcp/sessionMcp.test.ts

@@ -709,8 +709,19 @@ describe("session filesystem path boundaries over MCP", () => {
       name: "export_evidence_bundle",
       arguments: { path: "relative-bundle.json" },
     });
-    expect(exported.isError, JSON.stringify(exported.content)).toBe(true);
-    expect(JSON.stringify(exported.content)).toContain("absolute");
+    expect(parseMcpToolError(exported).error).toMatchObject({
+      code: "invalid_request",
+      details: {
+        operation: "export_evidence_bundle",
+        issues: [
+          expect.objectContaining({
+            path: ["path"],
+            reason: "invalid_format",
+            expected: "regex",
+          }),
+        ],
+      },
+    });
 
     const opened = await mcp.callTool({
       name: "open_binary",
@@ -721,8 +732,19 @@ describe("session filesystem path boundaries over MCP", () => {
       name: "close_binary",
       arguments: { snapshot_path: "relative-analysis.json" },
     });
-    expect(closed.isError, JSON.stringify(closed.content)).toBe(true);
-    expect(JSON.stringify(closed.content)).toContain("absolute");
+    expect(parseMcpToolError(closed).error).toMatchObject({
+      code: "invalid_request",
+      details: {
+        operation: "close_binary",
+        issues: [
+          expect.objectContaining({
+            path: ["snapshot_path"],
+            reason: "invalid_format",
+            expected: "regex",
+          }),
+        ],
+      },
+    });
     await mcp.callTool({ name: "close_binary", arguments: {} });
   }, 10_000);
 });

tests/boundary/mcp/wasmArtifactMcp.test.ts

@@ -383,7 +383,7 @@ it("attributes rejected WASM paths to their selected fields before provider work
     },
   });
   onTestFinished(harness.close);
-  for (const [input, paths] of [
+  const relativeCases = [
     [{ path: "relative.wasm" }, [["path"]]],
     [
       { path: value.artifact.path, glue_paths: ["relative.js"] },
@@ -412,7 +412,9 @@ it("attributes rejected WASM paths to their selected fields before provider work
       },
       [["path"], ["glue_paths", 0], ["candidate_paths", 0]],
     ],
-  ] as const) {
+  ] as const;
+  const checked: string[] = [];
+  for (const [input, paths] of relativeCases) {
     const response = await harness.client.callTool({
       name: "inspect_wasm_artifact",
       arguments: input,
@@ -423,14 +425,19 @@ it("attributes rejected WASM paths to their selected fields before provider work
       .object({ issues: z.array(z.unknown()) })
       .parse(failure.details);
     expect(issues).toEqual(
-      paths.map((path) => ({
-        path,
-        reason: "invalid_format",
-        expected: "regex",
-        message: "must be an absolute local filesystem path",
-      })),
+      paths.map((path) =>
+        expect.objectContaining({
+          path,
+          reason: "invalid_format",
+          expected: "regex",
+        }),
+      ),
     );
+    checked.push(paths.map((path) => path.join(".")).join("+"));
   }
+  expect(checked).toEqual(
+    expect.arrayContaining(["path", "glue_paths.0", "candidate_paths.0"]),
+  );
   expect(inspect).not.toHaveBeenCalled();
   const valid = await harness.client.callTool({
     name: "inspect_wasm_artifact",
@@ -760,12 +767,13 @@ it("rejects malformed paths, refuses WASM summary delivery before provider work
     expect(
       z.object({ issues: z.array(z.unknown()) }).parse(rejected.details).issues,
     ).toEqual(
-      [["path"], ["glue_paths", 0]].map((path) => ({
-        path,
-        reason: "invalid_format",
-        expected: "regex",
-        message: "must be an absolute local filesystem path",
-      })),
+      [["path"], ["glue_paths", 0]].map((path) =>
+        expect.objectContaining({
+          path,
+          reason: "invalid_format",
+          expected: "regex",
+        }),
+      ),
     );
     expect(inspect).not.toHaveBeenCalled();
     for (const input of [

tests/boundary/providers/desktopExportJsonDepth.test.ts

@@ -0,0 +1,205 @@
+import { execFileSync } from "node:child_process";
+import { writeFile } from "node:fs/promises";
+import { join } from "node:path";
+
+import { expect, it } from "vitest";
+
+import {
+  PYTHON_HELPERS,
+  PYTHON_IMPORTS,
+} from "../../../src/domain/desktop/appExportPython.js";
+import {
+  detectStateFormat,
+  textualView,
+} from "../../../src/domain/desktop/stateFormats.js";
+import { createTestTempDirectory } from "../../fixtures/temporaryDirectory.js";
+
+const arrays = "[".repeat(1500) + "1" + "]".repeat(1500);
+const objects = '{"a":'.repeat(1500) + "1" + "}".repeat(1500);
+const cases = [
+  ["discarded arrays", `{"value":${arrays},"value":"done"}`, true],
+  ["discarded objects", `{"value":${objects},"value":"done"}`, true],
+  ["escaped duplicate key", `{"val\\u0075e":${arrays},"value":"done"}`, true],
+  ["retained deep value", `{"value":${arrays}}`, false],
+  [
+    "retained deep inexact number",
+    `{"value":${"[".repeat(600)}9007199254740993${"]".repeat(600)}}`,
+    false,
+  ],
+  [
+    "deep overwritten inexact number",
+    `{"value":${"[".repeat(600)}{"x":9007199254740993,"x":1}${"]".repeat(600)}}`,
+    false,
+  ],
+  [
+    "deep empty-key overwrite",
+    `{"value":${"[".repeat(600)}{"":9007199254740993,"":1}${"]".repeat(600)}}`,
+    false,
+  ],
+  [
+    "deep multiple inexact keys with one overwritten",
+    `{"value":${"[".repeat(600)}{"a":9007199254740993,"b":9007199254740993,"a":1}${"]".repeat(600)}}`,
+    false,
+  ],
+  [
+    "deep multiple inexact keys all overwritten",
+    `{"value":${"[".repeat(600)}{"a":9007199254740993,"b":9007199254740993,"a":1,"b":2}${"]".repeat(600)}}`,
+    false,
+  ],
+  [
+    "deep inexact key replaced by inexact",
+    `{"value":${"[".repeat(600)}{"a":9007199254740993,"a":9007199254740995}${"]".repeat(600)}}`,
+    false,
+  ],
+  [
+    "deep escaped duplicate overwritten",
+    `{"value":${"[".repeat(600)}{"\\u0061":9007199254740993,"a":1}${"]".repeat(600)}}`,
+    false,
+  ],
+  [
+    "discarded deep inexact subtree",
+    `{"value":${"[".repeat(600)}9007199254740993${"]".repeat(600)},"value":"done"}`,
+    true,
+  ],
+  ["last admitted depth", "[".repeat(500) + "1" + "]".repeat(500), true],
+  ["empty container at limit", "[".repeat(501) + "]".repeat(501), true],
+  ["empty container over limit", "[".repeat(502) + "]".repeat(502), false],
+  ["trailing comma", `{"value":${arrays},"value":"done",}`, false],
+  ["missing value", `{"value":${arrays},"value":}`, false],
+  ["wrong closing bracket", `{"value":${arrays},"value":"done"]`, false],
+] as const;
+
+it.each(cases)("reads JSON with %s", async (_name, text, readable) => {
+  const root = await createTestTempDirectory("desktop-json-depth-");
+  const script = join(root, "read.py");
+  const imports = PYTHON_IMPORTS.split("\n")
+    .filter((line) => !line.includes("agentenv_protocol"))
+    .join("\n");
+  await writeFile(
+    script,
+    `${imports}${PYTHON_HELPERS}
+text = json.load(sys.stdin)
+print(json.dumps(_text_view("state.json", text, len(text.encode("utf-8")))))
+`,
+  );
+  const output = JSON.parse(
+    execFileSync(
+      process.platform === "win32" ? "python" : "python3",
+      ["-I", "-B", "-X", "utf8", script],
+      { input: JSON.stringify(text), encoding: "utf8" },
+    ),
+  ) as { format: string; view: unknown; error?: string };
+  const bytes = Buffer.from(text);
+  const format = detectStateFormat("state.json", bytes);
+  if (format !== "json" && format !== "text")
+    throw new Error(`Unexpected native format ${format}`);
+  const native = textualView(format, bytes);
+  expect(format === "json" && native.ok).toBe(readable);
+  expect(output.format).toBe(format);
+  if (native.ok) {
+    expect(output.error).toBeUndefined();
+    // Compare JSON values on their wire form, independent of object prototypes.
+    expect(JSON.stringify(output.view)).toBe(JSON.stringify(native.value));
+    if (
+      readable &&
+      (_name.startsWith("discarded") || _name === "escaped duplicate key")
+    )
+      expect(output.view).toEqual({ value: "done" });
+  } else {
+    expect(output.view).toBeNull();
+    expect(output.error).toBe(native.error);
+  }
+});
+
+it("bounds construction before refusing retained excessive JSON depth", async () => {
+  const root = await createTestTempDirectory("desktop-json-construction-");
+  const script = join(root, "bounded.py");
+  const imports = PYTHON_IMPORTS.split("\n")
+    .filter((line) => !line.includes("agentenv_protocol"))
+    .join("\n");
+  await writeFile(
+    script,
+    `${imports}${PYTHON_HELPERS}
+import tracemalloc
+text = "[" * 20_000 + "0" + "]" * 20_000
+recursion_limit = sys.getrecursionlimit()
+tracemalloc.start()
+entry = _json_view(text, len(text))
+peak = tracemalloc.get_traced_memory()[1]
+tracemalloc.stop()
+print(json.dumps({"entry": entry, "peak": peak, "recursion_unchanged": sys.getrecursionlimit() == recursion_limit}))
+`,
+  );
+  const output = JSON.parse(
+    execFileSync(
+      process.platform === "win32" ? "python" : "python3",
+      ["-I", "-B", "-X", "utf8", script],
+      { encoding: "utf8" },
+    ),
+  ) as { entry: unknown; peak: number; recursion_unchanged: boolean };
+  expect(output.entry).toEqual({
+    format: "json",
+    view: null,
+    error: "nested deeper than the 500 levels a JSON view keeps",
+  });
+  expect(output.recursion_unchanged).toBe(true);
+  // Python heap only, excluding source construction and interpreter/OS memory.
+  // A value retained only to refuse it must not allocate every input container.
+  expect(output.peak).toBeLessThan(1024 * 1024);
+});
+
+it("bounds allocations when a very deep value is overwritten", async () => {
+  const root = await createTestTempDirectory("desktop-json-memory-");
+  const script = join(root, "read.py");
+  const imports = PYTHON_IMPORTS.split("\n")
+    .filter((line) => !line.includes("agentenv_protocol"))
+    .join("\n");
+  await writeFile(
+    script,
+    `${imports}\nimport tracemalloc\n${PYTHON_HELPERS}
+text = '{"value":' + '[' * 200000 + '1' + ']' * 200000 + ',"value":"done"}'
+tracemalloc.start()
+result = _json_view(text, len(text))
+_, peak = tracemalloc.get_traced_memory()
+print(json.dumps({"view": result["view"], "peak": peak}))
+`,
+  );
+  const measured = JSON.parse(
+    execFileSync(
+      process.platform === "win32" ? "python" : "python3",
+      ["-I", "-B", script],
+      { encoding: "utf8", timeout: 30000 },
+    ),
+  ) as { view: unknown; peak: number };
+  expect(measured.view).toEqual({ value: "done" });
+  expect(measured.peak).toBeLessThan(8 * 1024 * 1024);
+}, 40000);
+
+it("bounds a wide container already beyond the retained view depth", async () => {
+  const root = await createTestTempDirectory("desktop-json-wide-depth-");
+  const script = join(root, "read.py");
+  const imports = PYTHON_IMPORTS.split("\n")
+    .filter((line) => !line.includes("agentenv_protocol"))
+    .join("\n");
+  await writeFile(
+    script,
+    `${imports}\nimport tracemalloc\n${PYTHON_HELPERS}
+text = '[' * 501 + ','.join(['"abc"'] * 600000) + ']' * 501
+tracemalloc.start()
+result = _json_view(text, len(text))
+_, peak = tracemalloc.get_traced_memory()
+print(json.dumps({"error": result.get("error"), "peak": peak}))
+`,
+  );
+  const measured = JSON.parse(
+    execFileSync(
+      process.platform === "win32" ? "python" : "python3",
+      ["-I", "-B", script],
+      { encoding: "utf8", timeout: 30000 },
+    ),
+  ) as { error: string; peak: number };
+  expect(measured.error).toBe(
+    "nested deeper than the 500 levels a JSON view keeps",
+  );
+  expect(measured.peak).toBeLessThan(8 * 1024 * 1024);
+}, 40000);

tests/boundary/providers/desktopExportPython.test.ts

@@ -34,7 +34,7 @@ const execPython = (
   try {
     writeFileSync(script, args[codeIndex + 1]!, "utf8");
     return execFileSync(
-      "python3",
+      process.platform === "win32" ? "python" : "python3",
       [
         "-X",
         "utf8",
@@ -375,15 +375,16 @@ it("checks text for JSON the way REA does, token by token, without parsing it",
         "-I",
         "-B",
         "-c",
-        `${imports}${PYTHON_HELPERS}\nprint(json.dumps([_is_json(text) for text in json.load(sys.stdin)]))`,
+        `${imports}${PYTHON_HELPERS}\ntexts = json.load(sys.stdin)\nprint(json.dumps({"syntax": [_read_json(text, build=False) is not _INVALID_JSON for text in texts], "built": [_read_json(text) is not _INVALID_JSON for text in texts]}))`,
       ],
       { input: JSON.stringify(texts), encoding: "utf8" },
     ),
-  ) as boolean[];
+  ) as { syntax: boolean[]; built: boolean[] };
 
   const parsed = texts.map((text) => safeParseJson(text).ok);
   expect(texts.map((text) => isJsonText(text))).toEqual(parsed);
-  expect(python).toEqual(parsed);
+  expect(python.syntax).toEqual(parsed);
+  expect(python.built).toEqual(parsed);
   expect(parsed.filter(Boolean)).toHaveLength(10);
 });
 
@@ -445,9 +446,13 @@ print(json.dumps([_text_view("settings.ini", text, len(text.encode()))["view"]["
   const root = await createTestTempDirectory("rea-keyfile-python-");
   const script = join(root, "fixture.py");
   await writeFile(script, program, "utf8");
-  const output = execFileSync("python3", ["-I", "-B", "-X", "utf8", script], {
-    input: JSON.stringify(inputs),
-    encoding: "utf8",
-  });
+  const output = execFileSync(
+    process.platform === "win32" ? "python" : "python3",
+    ["-I", "-B", "-X", "utf8", script],
+    {
+      input: JSON.stringify(inputs),
+      encoding: "utf8",
+    },
+  );
   expect(JSON.parse(output)).toEqual(inputs.map(keyfileView));
 });