* feat(ghidra): make the startup deadline configurable
Large binaries (an 8 MB PE with about 20,000 functions) need more than the
fixed 330 s for import and full auto-analysis, so every first request timed
out. REA_GHIDRA_STARTUP_TIMEOUT_MS overrides the deadline in milliseconds;
absent, empty or invalid values keep the 330 s default.
* docs(ghidra): document REA_GHIDRA_STARTUP_TIMEOUT_MS
* fix(ghidra): parse startup deadlines through runtime configuration
---------
Co-authored-by: morluto <76467478+morluto@users.noreply.github.com>
Retain complete authenticated application Evidence when the repeated MCP representation exceeds the default receive frame or Node string limit. Return a typed transport constraint, keep useful followup queries available, and stream full canonical bundles to atomic destinations.
Verify complete Notion and Obsidian workflows on Linux and native Windows, full CLI/Evidence parity, and real large Chrome screenshot recovery. Preserve complete success contracts and caller-selected evidence paths.
Refs #1065, #1053.
* fix(mcp): advertise JSON values without recursive schemas
`z.json()` projects a self-referential `$defs/__schema0` entry. Twenty
tool input schemas and 123 output schemas carried it, and clients or
model APIs that reject recursive JSON Schemas refuse the whole tool
list. Every JSON value satisfies `{}`, so the shared JSON value schema
now advertises that. Runtime parsing still admits only JSON values.
Refs #919
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
* fix(mcp): keep advertised input schemas within model function-calling limits
Some model providers reject the whole tool list when any input schema
contains a recursive $ref or nests deeper than 10 levels (fixes#919).
Sanitize the advertised wire projection: break cyclic $refs, bound nesting
depth, and drop unreachable $defs. Canonical Zod contracts are untouched.
---------
Co-authored-by: Kaoru0822 <208281322+kaoru0822-kitauji@users.noreply.github.com>
Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
Co-authored-by: sx4im <sx4im@users.noreply.github.com>
Co-authored-by: N0zoM1z0 <1705004398@qq.com>
## 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.
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)
* 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.
Ysopwnable