* feat(ghidra): edit function annotations atomically
Return annotation readback and refreshed function analysis through CLI and MCP. Own each database transaction, invalidate caches and immutable snapshots, preserve executable bytes, and retain the Windows mutation boundary.
Assisted-by: Nitori (gensokyo-skills:nitori-reverse-engineering)
* fix(ghidra): preserve qualified function annotation identity
Preserve namespaces during local name writes and match qualified readback to the refreshed dossier. Add a producer-shaped regression and verify a real namespaced C++ function through the CLI.
Assisted-by: Nitori (gensokyo-skills:nitori-reverse-engineering)
* test(ghidra): align verification with annotation authority
Keep strict capability and profile checks while admitting the explicit session metadata operation. Verify packaged transport authority and atomic transaction commitments and preserve a read-only Windows expectation.
Assisted-by: Nitori (gensokyo-skills:nitori-reverse-engineering)
* feat(ghidra): admit explicit DOS COM analysis
Carry caller-selected COM interpretation through CLI, MCP and target
identity, seed real-mode entry/context before Ghidra analysis, and verify
complete loaded bytes, source mappings and measured register context.
Keep original binaries unchanged and PSP/runtime coverage explicit.
Assisted-by: Nitori (gensokyo-skills:nitori-reverse-engineering)
* fix(verification): validate COM package selection before allocating fixtures
* feat(ghidra): verify DOS load images and expose memory evidence
Verify measured source bytes, mapped regions, fixups and entries against
the immutable MZ snapshot, retaining independent checks and raw evidence.
Expose loaded byte reads and authoritative original file offsets through
both CLI and MCP, with focused and actual Ghidra DOS verification.
Assisted-by: Nitori (gensokyo-skills:nitori-reverse-engineering)
* fix(cli): describe memory inspection arguments
* test(ghidra): align bridge fixtures and CLI capability accounting
typescript 5.9.3 to 7.0.2, vitest 4.1.10 to 5.0.3 (plus
@vitest/coverage-v8 and @fast-check/vitest 0.5.0 for peer compat),
@Modelcontextprotocol/client and server 2.0.0 to 2.3.1. Migrate the
removed describe.sequential to concurrent:false and regenerate
package metadata and product catalog.
Also restore byte-faithful reads in parseCliJsonInput: the safeJson
migration dropped the fatal UTF-8 check from #613. Vitest 5 requires
Node 22/24/26+, so verify on Node 24 (repo-pinned toolchain).
## Changes
Related to #545 and the permission-system removal in #555.
- Upgrade the shipped skill to v24 and remove obsolete filesystem grants, per-call approval flags, Electron file-root configuration, and DMG approval flags. Calls follow the user-requested investigation directly. Keep setup plan confirmation, actual OS requirements, and process/archive lifecycle boundaries.
- Correct the passive browser guide: endpoint/scope come from requests; ordinary local URL queries are retained, while credentials remain redacted.
- Audit canonical tool effects: declare possible DMG process/temp-directory effects, mark fresh extraction non-idempotent, and mark comparisons of supplied captures/PNGs as closed-world. Align artifact-provider capability effects with temporary mount-directory writes.
- Retain non-read-only hints for calls that add Evidence to the session; document that annotations are hints and that clients control their confirmation UI. Do not mislabel session mutations as read-only to suppress prompts.
- Regenerate package, skill, MCP, and product metadata from source.
## Verification
- `npm run test:focused -- <11 affected test files>`: **40 tests passed**, including skill transaction/backup/idempotence, SDK tools/list annotations, actual local capture/PNG comparisons, artifact extraction/containment/cancellation, DMG launcher/cleanup seam, setup confirmation, browser MCP and scenario MCP, CLI catalog parity.
- `npm run check`: typecheck, lint, format, knip, package metadata.
- `npm run docs:check`: generated catalogs, skill metadata, documentation facts, completion ledger, error schema.
No local real Hopper/Ghidra run: their adapters and analysis operations are unchanged. Native macOS DMG behavior is covered locally through the launcher seam; no local macOS/hdiutil claim is made.
Real browser verification passed using existing Headless Chrome143.0.7499.4: actual CLI/stdio MCP,9,331,407-byte PNG, passive capture/source maps, and owned/external scenario cleanup. An initial full Chrome143 run failed the existing screenshot-height assertion (1397 versus1536); the dedicated headless-shell run passed the complete verifier without code changes. The verifier run-lineage field remained unavailable; no lineage-coverage claim is made. Browser download into `.codex` was blocked by CDN403, so the successful run used an existing browser without changing host configuration.
* fix(browser): derive source-map imports from syntax nodes
Signed-off-by: Rudy Celekli <47457359+rudycelekli@users.noreply.github.com>
* fix(browser): recover source-map dependencies from decorated and aliased sources
Discarding a source's edges whenever it had parse errors cost more than it
protected. parseJavaScriptSource only enabled jsx and typescript, so a
decorated TypeScript source did not parse at all and contributed no edges at
all, even for the imports Babel could otherwise have read. That is the common
shape for the bundles this boundary inspects. "decorators-legacy" is enabled
instead of "decorators" because the standard form still rejects parameter
decorators such as constructor(@Inject() private s: S), which is the Angular
and Nest dependency-injection shape.
import x = require("m") parses cleanly but is a TSImportEqualsDeclaration
rather than a call expression, so it contributed no edge. It is now read as a
require dependency. It is only legal at module top level and always refers to
the host loader, so it needs no unbound-require check; the local-alias form
imports an entity name and still declares nothing.
A source whose syntax could not be recovered now yields status "partial" with
a limitation naming the affected sources, instead of an included item whose
empty edge list was indistinguishable from a source that genuinely imports
nothing. Edges that did parse are retained and the caller is told the list is
a subset, which matches how the static and semantic analysers already report
recovered syntax.
The source-map item status union gains "partial" and the coverage rollup now
counts it as retained, so a collection of only-partial items reports partial
rather than unavailable.
* Merge main into fix(browser): derive source-map imports from syntax nodes
Resolve the generated-file conflicts by taking main's generated output and
regenerating from the merged source contracts, rather than merging generated
text by hand.
---------
Signed-off-by: Rudy Celekli <47457359+rudycelekli@users.noreply.github.com>
Co-authored-by: morluto <76467478+morluto@users.noreply.github.com>
* fix(comparisons)!: preserve unknowns across partial observations
Share absence and digest semantics, keep unobserved managed bodies unknown, and match unique managed type/name/signatures before structural fallback.
BREAKING CHANGE: Managed comparison metadata adds exact-signature matching and its count, and name_matching now reports exact-signature-fallback.
* fix(javascript): preserve projected result binding semantics
Share syntax-aware property reads and assigned-result resolution. Retain destructuring paths and downgrade downstream whole-result relationships instead of resolving nested or wrapped calls as aliases.
* fix(native)!: admit complete parser values and preserve typed failures
Decode Mach headers by named columns, validate complete slice keys and lipo alignment, and preserve codesign runtime flags and tagged parser errors. Rename the Ghidra test dossier fixture and connect fake-backed suites to real verification lanes.
BREAKING CHANGE: Native load-command results no longer contain the unused, always-null file_offset field.
* fix(process): preserve host identity and actionable boundary failures
Thread selected platform and environment through process and Doctor seams, stamp observed producer identity in Evidence, and retain PTY, filesystem, lease and lazy-provider failure causes. Drain cancelled lazy loads and omit exited descendants from verified lineage.
* fix(browser): preserve cleanup and document-transition evidence
Make V8 and Playwright teardown cancellation-aware, expose primary failures alongside incomplete cleanup, share frame-tree and navigation rules, and clear stale WebMCP registrations without pruning unrelated child frames.
* fix(adapters): align managed targets and typed CLI outcomes
Inspect managed PE/CLI targets independently of native provider selection, reuse successful managed selections, and keep evidence bound to the actual inspected target. Classify canonical CLI error envelopes and exhaustive setup/update/uninstall outcomes, audit registered CLI coverage, and assert platform-specific runtime results.
* docs: refresh boundary contracts and shipped roadmap behavior
Return complete canonical Evidence records inline, including normalized_result, and preserve direct comparison and retained bundle identity.
Verified full deterministic gate, real Linux Ghidra CLI/MCP and independently installed artifact, generic package acceptance, private local samples, and targeted updates after syncing main.
Closes#551
Assisted-by: Kogasa (gensokyo-skills:kogasa-surprise-testing)
* feat(setup)!: expand agent integrations and simplify onboarding
Add native configuration formats for OpenCode, Antigravity, GitHub Copilot
CLI, VS Code, and Devin. Preserve JSONC comments and unrelated settings
while making setup and uninstall ownership-aware and idempotent.
Select agent targets before planning, separate discovery from intent, and
keep agent-only setup independent of optional provider prerequisites.
Cover configuration boundaries and interactive behavior in packaged checks.
BREAKING CHANGE: unscoped setup refreshes only existing REA-owned
registrations. Use --all-detected to configure every detected client.
Setup JSON contains a compact doctor summary; use rea doctor for full
diagnostics. Cancellation and successful dry runs now exit successfully.
* feat(cli)!: replace upgrade with verified updates
Resolve an exact release through npm's configured registry, update only the
identified installation, and verify its new executable before reporting success.
Return a read-only maintenance plan for existing enabled REA integrations.
BREAKING CHANGE: replace rea upgrade with rea update; no alias is retained.
Successful update JSON uses status "updated", reports the verified installed
version, and returns an unapplied maintenance plan instead of opening setup.
Correlate typed labels with recovered block entries and one indirect dispatch.
Preserve ambiguous and nonexact integer associations as unknown with raw diagnostics.
Expose defaults separately, collect backing load metadata, and invalidate old profiles.
Add independent compiler-byte CLI/MCP acceptance and actual Ghidra model controls.
Assisted-by: Kogasa (gensokyo-skills:kogasa-surprise-testing)
Assisted-by: Suika (gensokyo-skills:suika-scatter-gather-planning)
* fix(hopper): report unavailable procedure body coverage
* refactor!: simplify runtime tools and remove replay engines
Keep direct inspection, capture, and comparison tools. Bind handlers to named contracts and let agents compose experiments with commands and local fixture servers.
BREAKING CHANGE: Remove controlled replay, Node characterization, finite replay-machine, managed runtime planning, and redundant string-tracing tools. Retire process replay, shims, reactive scenarios, custom checkpoints, and active browser replay and origin-scope inputs.
Validate DOS MZ load modules and import them with Ghidra's 16-bit
real-mode profile. Preserve complete observed inclusive function body
ranges through inventory, function analysis, Evidence and snapshots.
Add a public source-generated DOS CLI/MCP verification lane and
regressions for malformed headers, body membership and cache profiles.
Assisted-by: Kogasa (gensokyo-skills:kogasa-surprise-testing)
Assisted-by: Suika (gensokyo-skills:suika-scatter-gather-planning)
Addresses #548 and #545.
#548: processScenarioSchema required a leading "/" for executable,
working_directory and filesystem_roots, so no process scenario could be
expressed on Windows at all. The report suggested node:path's isAbsolute, but
that answers for the host running the check: on Linux `C:\tools` is not
absolute, so a scenario captured on Windows would fail validation when it is
replayed, compared, or asserted in a test on another host. A boundary schema
must not vary with its evaluator, so the check accepts the POSIX form, a
Windows drive path and a UNC share everywhere. The rejection message now names
the constraint instead of leaving the caller to infer it from "invalid request".
The HTTP `path` field inside `checkpoints` is an URL path and is deliberately
left alone.
I checked whether this merely moved the failure downstream: containment is
enforced by isPathWithinRoot, which already uses host-aware path.relative, so
validation really was the only blocker.
#545: when a scope is inside the administrator ceiling but no grant was ever
issued, the denial still pointed at widening the ceiling -- advice that cannot
help, since the ceiling already permits the operation. The `missing` payload is
computed against candidate *grants*, so it describes what a grant must cover,
not a ceiling gap. `PermissionRemediation` gains a `grant` variant saying
exactly that, and PermissionAuthority selects it when the denial is not a
ceiling violation. An explicitly requested remediation is still honoured, and a
genuine ceiling violation still says "configure".
Keep explicitly selected Node Inspector targets observable when discovery
cannot verify their file location. Resolve literal POSIX discovery paths
without URI decoding, and retain lossy Windows or underscore paths as
unresolved metadata. Validate scriptParsed file URLs independently.
Preserve unknown target identity through runtime reconciliation, regenerate
contracts, and verify real CLI/MCP behavior on Linux and Windows.
Closes#530
Assisted-by: Kogasa (gensokyo-skills:kogasa-surprise-testing)
Replace empty tuples with a shared empty-array schema. Validate all input
and output schemas against Draft 2020-12 during catalog generation and
packaged MCP verification, with runtime and catalog regression coverage.
Closes#528
Assisted-by: Kogasa (gensokyo-skills:kogasa-surprise-testing)
* refactor(test): colocate pure-domain tests and reduce test debt
Move focused immutable domain/contracts/adapter tests from
tests/composition/** beside their production owners under src/** as
colocated *.test.ts/*.fixture.ts, and relocate persistence-shaped
composition tests under tests/boundary/filesystem/**. Update import
paths, the Vitest project topology (shared worker context for pure
domain/contracts and recording-port service projects), the test
migration ledger, testing docs, and AGENTS.md to match.
Generated with [Devin](https://devin.ai)
Co-Authored-By: Devin <158243242+devin-ai-integration[bot]@users.noreply.github.com>
* docs: remove test migration ledger
The cutover is complete and the ledger is no longer referenced anywhere
in source, scripts, or the docs gate. Drop the standalone artifact.
Generated with [Devin](https://devin.ai)
Co-Authored-By: Devin <158243242+devin-ai-integration[bot]@users.noreply.github.com>
* docs: clean up stale migration artifacts
Remove empty directories left by the test migration and replace the
"final cutover" language in docs/testing.md with standing PR guidance
that no longer references the completed migration.
Generated with [Devin](https://devin.ai)
Co-Authored-By: Devin <158243242+devin-ai-integration[bot]@users.noreply.github.com>
* fix: repair CI failures from schema, knip, and stale generated artifacts
Three root causes fixed:
1. catalog-schemas.mjs: valuesAt only traversed anyOf from Zod's
toJSONSchema, not oneOf. The webScreenshotDiffSchema change to a
discriminated union produces oneOf, so the product catalog generator
could not derive the web_screenshot_diff schema version. Add oneOf
traversal.
2. conformancePackage.ts: the test rewrite removed the only imports of
ScenarioManifest, ReplayPlan, ShimPlan, and ExpectedEvidence, making
them unused exports that knip flags. Remove the dead type aliases.
3. Regenerate stale artifacts (product catalog, MCP tool catalog, skill
metadata, conformance manifest) that drifted from the source changes.
Generated with [Devin](https://devin.ai)
Co-Authored-By: Devin <158243242+devin-ai-integration[bot]@users.noreply.github.com>
---------
Co-authored-by: Devin <158243242+devin-ai-integration[bot]@users.noreply.github.com>
N0zoM1z0
morluto
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github-actions[bot]
Rudy Mizrahi Celekli