Classify replacement EINVAL at the readlink syscall so the reader and importer
retain sibling observations. Give an admitted root's enumeration failure its
own typed field, use it for unresolved symlink coverage, and project it as a
graph limitation instead of an invalid dot-path child entry. Keep admission,
cancellation and cleanup failures distinct.
Closes#5135Closes#5136
BREAKING CHANGE: Partial reference-source reader results report failed root
enumeration in rootFailure instead of a failed directory child at path ".".
Historical source graphs preserve the root failure as a top-level limitation.
* fix(cleanup): preserve owner recovery instructions
Keep cleanup remediation through combined errors and direct or managed one-shot analysis while retaining primary diagnostics.
Refs: #4227
* fix(hopper): recover late startup and retained cleanup
Authenticate initial and cleanup handshakes through the same identity owner. Expose startup and cleanup activity, retain health after target retirement, and expire abandoned unauthenticated listeners without timing out authenticated work.
Refs: #4227
* fix(providers): retain composite lifecycle facts across retries
Preserve observed child health with incomplete peer coverage, retry only unresolved clients, and retain all child cleanup recovery actions.
Refs: #4233
* fix(process): honor cancellation through capture cleanup
Check the request signal after cleanup and before final publication, retaining completed observations under typed cancellation.
Refs: #4005
* fix(native): preserve failed LLDB launch ownership and exit proof
Publish failed-launch process identity and observed exit separately from object validity. Retire only the exact owned process and retain uncertainty when exit cannot be established.
Refs: #4232
* fix(native): honor cancellation after trace finalization
Check cancellation after runtime-root cleanup and retain collected trace observations as partial cancellation evidence.
Refs: #4009
* fix(cli): preserve analysis results when provider cleanup fails
Reuse the existing one-shot finalizer across thirteen command families to retain completed Evidence and primary diagnostics on close failure. Cover success, denied cleanup, and combined primary/cleanup failure through the public CLI.
Refs: #3935
* docs(lifecycle): define completion invariants and regression scenarios
Document distinct ownership/readiness/exit facts, late cancellation and atomic publication boundaries, partial child cleanup, and diagnostic retention. Link representative regressions and route contributor guidance through AGENTS.md.
Refs: #4227
* fix(session): retain run identity through pending cleanup
* fix(cli): preserve original cleanup resource diagnostics
* fix(native): retain completed facts through finalization failure
* fix(providers): report retained cleanup paths at their owners
* feat(kuna): serve procedures, pseudocode and assembly from Kuna exports
Register Kuna as a bring-your-own deep-analysis provider. It answers
list_documents, list_procedures, search_procedures, procedure_address,
address_name, procedure_pseudo_code, procedure_assembly and
analyze_function (and batch_decompile through composition) from the
verified project export. While a cold export builds in the background,
pseudocode comes from a single-function `kuna decompile` run on a private
copy and says so; assembly and data names wait for the export.
Each answer records its source and file span in raw_result, limitations
are scoped per operation, and the session-owned export is stopped on
close unless another session still waits for it. The literal/regex
procedure search predicate moves from the IDA runner into a shared
domain helper. `npm run verify:kuna` adds a real-provider lane with an
optional Ghidra comparison.
Refs #1957
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
* fix(kuna): refuse a Ghidra comparison without caller-built targets
Refs #1957
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
* fix(kuna): retry owned cleanup and keep answers bound to the opened Kuna
- Re-verify the Kuna executable's digest before every launch (memoized by
file identity), so no answer names one build while another produced it.
- Keep the process supervisor of an unproven stop, and retry it on every
later close in both the session and the cache; a failed close keeps
failing until the stop is proven instead of reporting success.
- Report an abandoned export's retained cleanup from session close.
- Forget and rebuild an adopted export whose files another REA process
evicted, instead of failing every later read.
- Close a private copy whose setup failed, and retry failed removals.
- Let the session own the shared quick inventory; each caller only stops
waiting when it cancels.
- Report a failed export as `failed` with its reason.
- Lane: release the MCP client when open_binary rejects a target, and accept
either valid source for the first answer.
Refs #1957
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
* fix(kuna): drain session requests before releasing workspaces
Combine caller cancellation with session shutdown and wait for active reads before releasing their process supervisors or private inputs. Retain unproven cleanup for later close attempts. Measure UTF-8 reply bytes without implying model token usage.
Co-authored-by: gensokyo-dev <342580529+gensokyo-dev@users.noreply.github.com>
Co-authored-by: Kaoru0822 <208281322+kaoru0822-kitauji@users.noreply.github.com>
* perf(kuna): keep document metadata reads free of target analysis
Listing the selected path no longer initializes the project cache or starts an export that the request never consumes.
Co-authored-by: gensokyo-dev <342580529+gensokyo-dev@users.noreply.github.com>
Co-authored-by: Kaoru0822 <208281322+kaoru0822-kitauji@users.noreply.github.com>
* fix(kuna): reject verification matrices with missing functions
Validate requested matrix coverage before building the fixture or opening providers. Empty matrices, unmatched names and partially matched function sets must fail instead of reporting an unperformed comparison as successful.
Co-authored-by: gensokyo-dev <342580529+gensokyo-dev@users.noreply.github.com>
Co-authored-by: Kaoru0822 <208281322+kaoru0822-kitauji@users.noreply.github.com>
* fix(kuna): retain component provenance in function dossiers
Record each source facet as one file span and preserve both pseudocode and assembly digests/ranges in combined reports. Keep direct text source fields compatible and verify every combined span through the real MCP lane.
Co-authored-by: gensokyo-dev <342580529+gensokyo-dev@users.noreply.github.com>
Co-authored-by: Kaoru0822 <208281322+kaoru0822-kitauji@users.noreply.github.com>
* fix(kuna): keep retired file cleanup bound to its export
Retain the export key with each failed file removal so a cancelled session reports and retries its own stopped resources. Preserve that association across sweeping and process-cleanup recovery without attributing unrelated cache failures to the session.
Co-authored-by: gensokyo-dev <342580529+gensokyo-dev@users.noreply.github.com>
Co-authored-by: Kaoru0822 <208281322+kaoru0822-kitauji@users.noreply.github.com>
* docs(kuna): document the Kuna provider and list it in the catalog (#3855)
* docs(kuna): document the Kuna provider and list it in the catalog
Add the Kuna provider guide (configuration, answered tools, cold and warm
paths, provenance, cache ownership, verification lane), link it from the
README and its translations, the CLI, installation and index pages and the
site navigation, describe `npm run verify:kuna` in the testing guide, credit
Kuna in THIRD_PARTY_NOTICES, teach the agent skill when to select Kuna, and
register its identity and operations in the generated product catalog.
Refs #1957
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
* docs(kuna): state the Linux cache fallback, raw_result scope and comparison inputs
Refs #1957
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
* docs(kuna): note that cache pins hold within one REA process
Refs #1957
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
* docs(kuna): describe retired staging and retried cleanup
Refs #1957
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
---------
Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
* fix(kuna): supervise regex and bind reads to one export
Share a cancellable ECMAScript matching worker with Hopper while preserving its error contract. Bind C and assembly indexes to immutable project readers, retry whole dossiers after eviction, and enforce the existing buffered-text capacity before allocating cached spans. Document the verified Linux scope and keep complete exports accessible.
Co-authored-by: gensokyo-dev <342580529+gensokyo-dev@users.noreply.github.com>
Co-authored-by: Kaoru0822 <208281322+kaoru0822-kitauji@users.noreply.github.com>
---------
Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
Co-authored-by: N0zoM1z0 <161784452+N0zoM1z0@users.noreply.github.com>
Co-authored-by: gensokyo-dev <342580529+gensokyo-dev@users.noreply.github.com>
* fix(cli): accept --flag=value for global output flags
`rea <command> --format=json` failed with "Unknown flag: --format".
`--filter-output=...`, `--token-limit=...` and `--token-offset=...`
failed the same way. Incur reads these global flags only in spaced form,
so the equals form fell through to the command parser. Command options
already accept both forms, and `rea mcp doctor` parses `--format=` itself.
A valued output flag with no value (`--format` last, or `--format=`)
also reported the flag as unknown with code UNKNOWN.
normalizeCliOutputArguments, in the module that owns output-argument
interpretation, now splits the equals forms of the four valued output
flags. The entry point passes the normalized argv to rea's output
validation and to Incur, so both read the same effective values. A
missing value now fails with MISSING_OUTPUT_VALUE and names the flag.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
* fix(cli): detect missing output values while parsing output flags
The missing-value check scanned argv again after parsing, so it also
checked tokens the parser had already consumed as values. For example,
`--filter-output --format` selects the field `--format`, yet the second
scan reported `--format` as missing a value. parseCliOutputArguments
now records the first valued flag it skips for lack of a value, in the
same pass that consumes values.
Cover normalizeCliOutputArguments directly: values containing `=`, empty
values, and command options that only share a prefix. Export it in the
dispatcher test's runtime stub as well.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
---------
Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
* fix(cli): stop quietly when the stdout reader closes early
`rea ... | head` crashed once head closed the pipe. TOON and YAML output
raised an unhandled EPIPE 'error' event with a Node stack trace. JSON
output reported {"code":"UNKNOWN","message":"write EPIPE"} on stderr.
Both exited 1, as if the analysis had failed.
The CLI entry point owns process.stdout, so it now treats EPIPE as the
reader declining the rest of the output. It stops writing, suppresses
the failure report and exits 141 like a SIGPIPE-terminated writer, also
when Incur exits through its own failure path. Other stdout errors are
handled as before.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
* fix(cli): guard mcp doctor output and cover midstream reader closure
The closed-reader guard was only installed for ordinary CLI commands. As a
result `rea mcp doctor | head` still crashed on EPIPE. The guard now lives
in one entry-point function shared by both CLI branches; MCP stdio keeps
its own lifecycle.
The tests now also close the reader after the first chunk of a 4 MiB
streamed JSON result, so later writes in writeJsonOutput are covered.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
---------
Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
Carry the concrete configuration and admission reason through the typed provider-selection error to CLI callers.
Fixes#3055.
Reviewed-PR: #3087
Co-authored-by: 1052326311 <65798732+1052326311@users.noreply.github.com>
Exercise real MCP navigation error delivery and preserve a custom caller abort cause through source-map cancellation. Document doctor stderr retention.
Co-authored-by: yasshmittal <myash0091@gmail.com>
* feat(native): read embedded cargo-auditable Rust dependency lists
* fix(native): trim PE section padding and compute dependency cycles iteratively
* fix(native): ignore SHT_NOBITS sections and validate dependency edges linearly
* fix(native): bound compiler path scanning and retained hashes
* fix(rust): pass package arrays as named parameterized test cases
* fix(rust): admit graph expansion and preserve resource units
* fix(rust): reject malformed packages, false cycles, and hidden compiler paths
Fail the first malformed cargo-auditable package before Zod collects an
issue per field. Require cyclic dependency indices to match the cycles in
package dependencies. Keep read-only ELF ranges when a section name does
not fit the bounded name window, so a rustc path in that range is still
reported.
* fix(ci): repair integrated checks and Hopper test baseline
* fix(go): verify Mach-O sections against segments
---------
Co-authored-by: Matt Van Horn <455140+mvanhorn@users.noreply.github.com>
Co-authored-by: morluto <76467478+morluto@users.noreply.github.com>
Co-authored-by: Cursor Agent <cursoragent@cursor.com>
* feat(ghidra): admit raw NMOS 6502 analysis
* test(ghidra): require verified POSIX verifier cleanup
* test(ghidra): verify 6502 low-memory raw imports
* docs(skill): document raw NMOS 6502 support
* fix(ghidra): preserve requested Windows raw source paths
* docs(ghidra): include raw 6502 in Windows installation scope
* test(ghidra): verify Windows raw junction rejection through CLI and MCP
* fix(validation): make fixtures portable and preserve explicit Codex home
* fix(ghidra): attest raw mapping state and address space
* fix(ghidra): align diagnostics and regression groups
* fix(ghidra): bind raw attestation to language address space
* chore(ghidra): avoid verifier insertion conflict
* docs(ghidra): align linked raw admission guides
* fix(ghidra): retain 6502 verifier workspace on failure
* test(ghidra): isolate Windows authority doctor fixture
* fix(binary): re-admit Windows raw paths on session reopen
* test(binary): require fresh provider execution after path change
* Constrain 6502 to raw lifecycle and snapshot targets
* Bypass saved reads for unadmitted Windows paths
* Guard direct CLI snapshot replay on Windows paths
* fix(snapshot): gate Windows Ghidra replay on native admission
* fix(snapshot): constrain nested 6502 subjects to raw images
* test: make dyld slice fixtures portable
* fix(reference): report sloppy scripts, PHP, C# and enclosing Git facts
Importing the source/ subtree of a legacy PHP and C# checkout produced
four wrong or missing facts:
- Babel's unambiguous mode parses a module first and keeps its
strict-mode recovery errors after falling back to a script, so a valid
sloppy-mode `delete messages;` was reported as a parse failure and the
semantic IR marked the file as parser-recovered. Parsing now goes
through one owner that re-parses such a script as a script.
- .php and .cs files had no language; they are now detected as PHP and
C# (detection only, no parsing).
- A root without its own .git was reported as having no version
control even inside a checkout. The adapter now resolves the nearest
enclosing repository, as Git does, and reports `none` only when no
ancestor has one.
- The CLI recorded importer_version as null although the package
version is known.
* fix(reference): keep module strictness and classify C# and PHP as source
Review follow-up. `.mjs` and `.mts` files are modules by extension, but
the script fallback re-parsed them in sloppy mode and erased real
strict-mode errors. The parser boundary now owns the extension rule,
parses explicit modules as modules and applies the fallback only when
the mode is ambiguous; the require-binding analysis uses the same rule.
`.cs` and `.php` received a language but stayed classified as unknown,
so source-to-bundle comparison dropped them. Both are now source
extensions, like the other detected languages.
* fix(reference): honor package module scope and keep unknown-mode strict errors
Review follow-up. A `.js` file under a package.json with `"type":
"module"` is an ES module, but it went through the script fallback that
erases strict-mode errors. The import now reads each in-inventory
package.json and parses `.js` files in a module scope as modules. Other
`.js` and `.ts` sources keep an unknown mode, because bundlers treat them
as modules without that field: they are no longer forced to script, and
errors that only the module parse reports are kept as an entry limitation.
* fix(reference): bound package scopes and keep application parsing unchanged
Review follow-up.
- `.cjs` files parse as scripts, so module-only strict errors no longer
become limitations on CommonJS trees. `.cts` keeps an unknown mode
because TypeScript compiles ES import syntax there.
- An unreadable or linked package.json now bounds the module scope with
an unknown type instead of letting an outer `"type": "module"` apply.
- The application pipeline parses as on main again. Its module-only
strict errors keep a source partial; package-mode handling stays in the
reference importer.
* refactor(reference): keep unmarked module modes unknown instead of resolving package scope
Review follow-up. Resolving Node package scope for `.js` kept pulling in
more of Node's lookup semantics (require bindings, excluded or
directory-named manifests). Only extensions now select a mode: `.mjs`
and `.mts` parse as modules and `.cjs` as scripts. Every other source
keeps an unknown mode, so module-only strict errors stay visible as an
entry limitation instead of being dropped or asserted. This matches the
require-binding analysis, which also treats unmarked paths as unknown.
Add offline SQLite database/WAL inspection through the shared CLI/MCP.
Use compact inventory, selected-table schema, exact ordered columns and
bounded row samples while preserving source identity and lossless values.
Retain completed Evidence through late cancellation and private-root cleanup
failures, bound concurrent inspections, and recheck journal validity after
acquisition. Reuse prepared CI runtime artifacts across supported Node lines.
Co-authored-by: Y0UW1SH <29498139+Y0UW1SH@users.noreply.github.com>
Assisted-by: Kogasa (gensokyo-skills:kogasa-surprise-testing)
Put setup, developer commands, MCP replies, and investigation recipes before
client details and implementation references. Preserve existing guide anchors,
examples, provenance, partial-result recovery, and provider restrictions.
Correct verified documentation drift, synchronize the Ghidra capability
wording, and regenerate metadata for skill version 40. Keep uncertain platform
and lifecycle findings unchanged. Refs #2156.
Validation: 56 focused tests, check:fast, docs:check, VitePress production build,
format and link/example checks. Real isolated CLI/MCP probes cover Ghidra,
NativeAOT, HAR, cancellation, Chrome, large ELF delivery, native type limits,
and the new JS/managed/process/setup recipes. Heavy work uses two CPUs;
a resource-heavy DOM probe was stopped and replaced by a smaller real CDP
payload-limit control. Windows, macOS GUI, ADB, and the full CI matrix were
not executed.
Co-authored-by: factory-droid[bot] <138933559+factory-droid[bot]@users.noreply.github.com>
Stop cached metadata replay before a provider write starts, including while its reply is pending or fails after applying the mutation. Keep snapshot import and export disabled until the target is reopened.
Validate failed replies, conflicting provider identity, and overlapping reads through the shared session boundary.
* feat(go): inspect embedded binary build metadata
* fix(go): preserve byte metadata and validate container mappings
* fix(go): support moduleless legacy build metadata
Recognize optional module string headers in declared zero-filled memory while rejecting ambiguous and unmapped pointers. Preserve the original module-pointer field as the zero-byte source anchor.
Classify initial symlink-loop and overlong-path failures as invalid input, with CLI and MCP regressions.
* fix(go): reject undersized PE optional headers
* fix(native): stabilize ELF memory checks and clean up exec wrappers
Use existing parent/group/run-token ownership for caller-selected Python launchers, which can exec through a shell or prlimit. Add cancellation regressions for the valid wrapper and wrong-parent/token cases.
Replace the timing-dependent 30,000-section memory workload with a valid 32 MiB padded ELF under a 64 MiB address-space limit. Check the same image successfully through CLI and MCP before requiring a typed memory failure, preserving the production timeout and all error assertions.
Validation: npm run check and check:fast passed; 61 focused tests passed including Go CLI/MCP and session snapshots. Real decoder probes with pinned packages passed on Python 3.12.3 and 3.12.14. The full local ELF verifier is blocked by this container's procps/process-ownership boundary; the exact pushed head requires GitHub's real-binary-layout lane.
* test: repair Electron fixtures and stabilize catalog startup checks
Declare Electron imports in option, preload override, and path-resolution fixtures after upstream began requiring proven API provenance. Retain all option and preload assertions and adjust exact source ranges for the added import line.
Use the existing bounded acceptance timeout for the cold catalog lifecycle test instead of a separate 15-second ceiling. This retains the coverage allowance and all catalog, error, and cleanup assertions without retries.
Validation: npm run check, final check:fast, formatting and diff checks passed. Source path regression and Go boundary/MCP/service checks passed. All 20 Go CLI cases and both supported-host runtime cases passed on rerun; two macOS-only cases skipped on Linux. A prior contended local run timed out once in a Go CLI diagnostic; that case passed on rerun. Electron process-boundary verification is blocked locally by procps namespace inspection and requires fresh CI.
* test(mcp): isolate nested schema references between tool contracts
Clear Ajv's non-meta schema registry after each root, including compilation failures. Disabling root registration alone leaves nested IDs available to later tools and can let a dangling reference pass the catalog gate.
Add regressions for leakage after successful and failed compilation while retaining shared meta-schema validators. The regression failed before the fix; all 11 schema cases and full npm run check pass. Reviewed independently.
* test(ci): align Go effects and source-map verification contracts
Audit the Go inspector wording as static metadata inspection. Assert retained source declaration indexes in BOM reconstruction and the compiler-derived nested-map oracle. Keep a 45,000-map admission control below the 32 MiB output budget and the 50,000-map overflow case above it with the expanded representation.
Validation: reproduced all four failing assertions, then passed 120 focused tests and the final admission suite. npm run check and real Chrome 154 / esbuild 0.25.10 source-map verification passed, including all four nested-map scenarios and verified process lineage.
---------
Co-authored-by: morluto <76467478+morluto@users.noreply.github.com>
* feat(native): admit raw binaries with caller-supplied architecture and entry
* fix(native): honor raw-binary preparation and entry identity
* fix(ghidra): stream raw snapshot attestation with cancellation
* fix(native): preserve and validate raw lifecycle entries
---------
Co-authored-by: morluto <76467478+morluto@users.noreply.github.com>
Record the exact matching pattern and distinguish project, default, caller, and configured-sensitive exclusions without changing ignore ordering. Include that provenance in graph commitments and validate the contract through compiled CLI and MCP consumers.
BREAKING CHANGE: Pattern-based reference graph exclusions require pattern and distinguish project-ignored and default-ignored reasons. Re-import saved graphs that omit matching patterns.
The skill's CLI fallback printed the complete application Evidence to
stdout. A real ASAR produces hundreds of megabytes (334 MB for Obsidian),
which an agent then reads into its context. Save the Evidence to a file
and project a summary or module page with inspect-analysis-view instead.
Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
`--json` / `--format json` always indented its streamed result. Agents and
scripts read REA through pipes and redirects, where indentation carries no
information: on real application results it added 16-45% model tokens
(o200k proxy) and 25-73% bytes. The skill's CLI fallback uses `--json`.
Indent only when stdout is a TTY, as `gh --json` does; piped or redirected
JSON is compact. The JSON value, `jsonl`, `--filter-output`,
`--full-output` and the token-window paths are unchanged. `jq .` restores
indentation for files.
Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
Select residual unknown histories as complete units and retain referenced registry mutation Evidence regardless of the active target at edit time. Prune incompatible dependency histories atomically instead of retaining stale dispositions.
Verify public MCP save/read/reopen for verified, withdrawn, and out-of-scope resolutions, and document target scope rules.
Deliver complete Evidence directly through MCP with required nullable analysis profiles and immutable per-server delivery settings. Bind selected environments at construction and require typed cleanup outcomes with retained retry ownership.
Remove test-only routing, duplicate session and snapshot metadata, producer-field repairs, and ambiguous provider arguments. Separate artifact byte identity from occurrence classification and retain typed source-map and partial native facts across CLI, MCP, and verifier consumers.
BREAKING CHANGE: obsolete Evidence envelopes, session aliases, incomplete snapshots, and missing normalized producer facts are no longer accepted.
* docs: simplify the English README
Preserve the opening and add the official skills.sh badge. Move setup diagnostics and CLI/Evidence details into guides, add three website showcases, and check setup-client facts in the installation guide.
Refs #1017
* docs: add README workflow and FAQ
Restore the original Disclaimer verbatim, invite community showcases, reuse the website investigation figure, and answer six common questions.
* docs: clarify README updates and collapse FAQ
* docs: welcome contributions in the README
* docs: highlight website guidance before quick start
* docs: keep README capability links aligned with main
* fix(docs): preserve README backlinks and release checks
morluto