* chore(deps): finish toolchain upgrades and drop dead weight
pino 9 to 10, @types/node 24 to 26, oxlint 1.73 to 1.87, knip 6.26
to 6.39, turbo 2.10 to 2.11. Narrow engines to supported majors
(22/24/26; vitest 5 refuses Node 25). Scope no-var-requires off for
Electron CJS hooks and fixtures.
Remove TypeDoc: incompatible with TypeScript 7 at install and
runtime, used by nothing in any gate. Drop the dep, docs:api
workflow, typedoc.json, CI artifact step, and related docs.
Replace graphology with a local call-graph adjacency plus BFS: the
only consumer is call-path search, and graphology-types ships no
types entry for TS7 NodeNext resolution. Delete both graphology
dependencies.
Remove dead re-exports newly flagged by knip 6.39.
* chore: drop stale typedoc and replay references
Remove the docs:api release-checklist step, the orphaned docs/api
ignore entry, and the nonexistent replay glob from the adapters
project.
Move each error family out of domain/errors.ts into its own module
(base, core, provider selection/adapter, browser observation,
artifact, evidence, unknown registry, hopper, configuration) and
relocate AnalysisErrorProjection to analysisErrorProjection.
Migrate all 162 importers to the owning modules and delete
errors.ts. No re-export shims; behavior is unchanged.
Move official, enhanced, and session contract arrays with their
builders into officialToolContracts, enhancedToolContracts, and
sessionToolContracts. toolContracts keeps the ordered assembly and
resolver. Migrate all importers including catalog scripts. No
re-export shims; generated catalog output is unchanged.
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).
* refactor(domain): consolidate canonical ordering and digest helpers (#624)
* refactor(domain): consolidate canonical ordering and digest helpers
Single owner for code-point ordering (domain/canonicalOrdering.ts)
and canonical JSON digests (domain/comparisonSemantics.ts). Delete
all local compareCodePoints/compareText/digestCanonical duplicates
and migrate every importer. No re-export shims.
* fix(ci): allow slower real browser startup
* chore(config): remove dead eslint, dedupe scripts, cacheable turbo tasks
Delete eslint.config.js (oxlint is the linter), drop lint:dead alias,
pin smol-toml, fold jscpd/scan:todos into check:pr, make test:run
cacheable, align oxlint ignores.
* fix(config): hash all test inputs for cached runs
* docs: fix architecture diagram and pretty-print tool catalog
Drop dangling REPLAY edges, add dotnet/reference/error/evaluation
nodes. Emit 2-space JSON from the catalog generator and regenerate.
* test: extract shared fixtures, drop knip carve-outs
Dedupe android/apple session tests, bundler adapter headers, and
reconstruction helpers into tests/support fixtures. Delete unused
type aliases and the knip ignoreIssues block. Lower jscpd threshold
2.7 to 2.5.
* refactor(app): split Setup and ProcessOwnership modules
Extract SetupTypes/SetupHost from Setup.ts and move observation
helpers into ProcessOwnershipObservation/ProcessTree. Migrate all
importers including CLI commands. No re-export shims.
* refactor(runtime): centralize safe JSON parsing and preserve error causes
Add domain/safeJson.safeParseJson and migrate all raw JSON.parse
call sites. Name catch causes and preserve failure reasons instead
of swallowing; annotate genuine best-effort cleanup.
* fix(runtime): retain JSON parse error causes
* refactor(domain): consolidate canonical ordering and digest helpers (#624)
* refactor(domain): consolidate canonical ordering and digest helpers
Single owner for code-point ordering (domain/canonicalOrdering.ts)
and canonical JSON digests (domain/comparisonSemantics.ts). Delete
all local compareCodePoints/compareText/digestCanonical duplicates
and migrate every importer. No re-export shims.
* fix(ci): allow slower real browser startup
* chore(config): remove dead eslint, dedupe scripts, cacheable turbo tasks
Delete eslint.config.js (oxlint is the linter), drop lint:dead alias,
pin smol-toml, fold jscpd/scan:todos into check:pr, make test:run
cacheable, align oxlint ignores.
* fix(config): hash all test inputs for cached runs
* docs: fix architecture diagram and pretty-print tool catalog
Drop dangling REPLAY edges, add dotnet/reference/error/evaluation
nodes. Emit 2-space JSON from the catalog generator and regenerate.
* test: extract shared fixtures, drop knip carve-outs
Dedupe android/apple session tests, bundler adapter headers, and
reconstruction helpers into tests/support fixtures. Delete unused
type aliases and the knip ignoreIssues block. Lower jscpd threshold
2.7 to 2.5.
* refactor(app): split Setup and ProcessOwnership modules
Extract SetupTypes/SetupHost from Setup.ts and move observation
helpers into ProcessOwnershipObservation/ProcessTree. Migrate all
importers including CLI commands. No re-export shims.
* refactor(domain): consolidate canonical ordering and digest helpers (#624)
* refactor(domain): consolidate canonical ordering and digest helpers
Single owner for code-point ordering (domain/canonicalOrdering.ts)
and canonical JSON digests (domain/comparisonSemantics.ts). Delete
all local compareCodePoints/compareText/digestCanonical duplicates
and migrate every importer. No re-export shims.
* fix(ci): allow slower real browser startup
* chore(config): remove dead eslint, dedupe scripts, cacheable turbo tasks
Delete eslint.config.js (oxlint is the linter), drop lint:dead alias,
pin smol-toml, fold jscpd/scan:todos into check:pr, make test:run
cacheable, align oxlint ignores.
* fix(config): hash all test inputs for cached runs
* docs: fix architecture diagram and pretty-print tool catalog
Drop dangling REPLAY edges, add dotnet/reference/error/evaluation
nodes. Emit 2-space JSON from the catalog generator and regenerate.
* test: extract shared fixtures, drop knip carve-outs
Dedupe android/apple session tests, bundler adapter headers, and
reconstruction helpers into tests/support fixtures. Delete unused
type aliases and the knip ignoreIssues block. Lower jscpd threshold
2.7 to 2.5.
* refactor(domain): consolidate canonical ordering and digest helpers
Single owner for code-point ordering (domain/canonicalOrdering.ts)
and canonical JSON digests (domain/comparisonSemantics.ts). Delete
all local compareCodePoints/compareText/digestCanonical duplicates
and migrate every importer. No re-export shims.
* fix(ci): allow slower real browser startup
Cancel ZIP extraction promptly when an unread consumer applies backpressure, releasing the producer instead of leaving it parked on a drain that can never arrive.
## 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(javascript): honor package exports condition order
Signed-off-by: Rudy Celekli <47457359+rudycelekli@users.noreply.github.com>
* fix(javascript): resolve exports against Node's full condition set
The declared-order fix selected targets against {default, import|require},
but Node's active set for the resolver that owns installed packages also
includes "node" and "node-addons". Ordering only means something against the
full active set, so a package declaring {"node", "import"} resolved to the
wrong target, and a package declaring only {"import"} reported no target
where Node resolves ./node.cjs.
Nested condition objects and fallback arrays are also valid Node targets.
They are now flattened in Node's own order: a condition object stops at its
first active key, so a null or unmatched nested target ends the search, while
an array skips the entries it cannot resolve and concatenates the rest. Node
does not fall through a target whose file is absent, so the first flattened
target stands and its absence is reported rather than skipped.
A valid exports map that matches no active condition is reported as external
with the declared condition names, and one that selects an unsupported nested
or array target no longer borrows the "not valid package JSON" reason.
The differential test installs a real package and resolves the same bare
specifier through Node and through REA, mirroring file presence between the
filesystem and the inventory. 18 of the 25 cases fail without this change.
* style: apply Prettier to the conditional exports differential test
---------
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)
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