Commit 5ac3dc96 re-added application workflow scenarios under tests/acceptance/applications that are already covered under tests/boundary (mcp, filesystem, process) via the shared tests/fixtures/applicationMcpHarness.js fixture, per the boundary classification in 0e0b386d. The duplicates added no new coverage and pushed the jscpd duplication gate over its 2.5% threshold, failing CI static checks.
Parses rea mcp doctor arguments against one zod option schema that is also the help renderer's source of truth, answering --help/-h in any position without starting a diagnostic session and keeping actionable errors for unknown options and invalid formats. Updates the landed help assertion to the schema-rendered format list and adds boundary coverage for help positioning and --format edge cases.
Adds an owned in-memory MCP harness plus acceptance coverage for trace/compare/export-shape workflows over inline and recorded Evidence, including rejection of mismatched evidence references and spoofed providers. All 16 scenarios pass on the current base.
* 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
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Co-authored-by: morluto <76467478+morluto@users.noreply.github.com>
Integrate the numeric precision correction from #1135 with complete supplemental
metadata handling. Keep decoded numbers with an explicit limitation for mixed XML
content or unclassified integer text, rather than assigning another literal's
exact decimal. Project nonnumeric UID and CF$UID dictionary values recursively
while preserving numeric references, graph identity and original byte digests.
Add filesystem, built CLI and MCP regressions for the review findings, adjacent
XML representations and numeric reference controls. Retain the original native
Foundation qualification fixtures and verifier.
Verification: 84 focused tests; npm run check; npm run docs:check;
npm run verify:test-discovery; npm run verify:keyed-archive (real Foundation,
CLI and stdio MCP). No real Hopper or Ghidra verification was needed or run.
Co-authored-by: Rudy Mizrahi Celekli <47457359+rudycelekli@users.noreply.github.com>
Signed-off-by: morluto <76467478+morluto@users.noreply.github.com>
* fix(javascript): omit self-referential import edges with disclosure
A specifier that resolves back to the importing module itself produced an
imports edge from a module to itself, which the application graph schema
forbids; one such specifier failed result validation and lost the whole
analysis. Skip those edges at composition time and disclose the omission
count in the graph limitations.
Fixes#1129
* test(javascript): verify self-import behavior through the compiled CLI
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Co-authored-by: BaaRai <baarai@users.noreply.github.com>
Co-authored-by: morluto <76467478+morluto@users.noreply.github.com>
* test(browser): pin DOM and source-map URL policy classifications
Cover the unsupported DOM scope, credentialed destinations, and the source-map fetcher's pre-request filtering of credentials, other origins and non-http(s) URLs, so a later vocabulary unification can show exactly what changes.
Refs #829
* test(browser): assert exact sanitized credentialed DOM URL
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Co-authored-by: morluto <76467478+morluto@users.noreply.github.com>
* fix(hopper): enforce caller-supplied request deadlines
* fix(hopper): correct idle deadline state and name timeout bound
Zero-ms deadlines never enter the FIFO, so report providerState
not_started instead of busy; the busy wording tells callers to wait
for an active request that does not exist. Name the Node timer
ceiling once and reuse it in validation and the error message.
* fix(hopper): enforce elapsed deadlines before dispatch and replies
* fix(hopper): distinguish unsent requests in timeout diagnostics
* test(hopper): exercise request deadlines against native Hopper
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Co-authored-by: Vilmer Frost <frost.vilmer@gmail.com>
Co-authored-by: morluto <76467478+morluto@users.noreply.github.com>
* fix(hopper): preserve owned basic-block endpoint instructions
* test(hopper): share probe runner and restore fixture hashability
Reuse one probe helper with the facade test's execFile options
(encoding, timeout, maxBuffer) instead of repeating the invocation.
Give the fixture Block a hash consistent with its equality so the
equality-based ownership doubles stay hashable.
* fix(hopper): align owned instruction walks with normalized block ranges
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Co-authored-by: Vilmer Frost <frost.vilmer@gmail.com>
Co-authored-by: morluto <76467478+morluto@users.noreply.github.com>
Adds README_fa.md (Persian/Farsi) contributed via PR #1140, keeps onboarding commands, links, and structure aligned with English, links فارسی from every translated selector, and registers fa in the readme consistency matrix.
Co-authored-by: Arad Ashkan <65897590+AradAshkan@users.noreply.github.com>
* fix(setup): treat empty client config files as new documents
An empty MCP config file (for example Antigravity's mcp_config.json, which
the client can create with zero bytes) was reported as malformed, which
blocked rea setup from configuring every other detected agent. Parse a
whitespace- or BOM-only JSON/JSONC file as an empty document and write a
fresh document over it.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
* test(setup): use explicit unicode escape for BOM-only empty config case
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Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
Co-authored-by: morluto <76467478+morluto@users.noreply.github.com>
* fix(update): accept npm 12 release metadata
(cherry picked from commit aa400d18c95e36029c5c654c396ec66924e1358f)
* fix(update): classify npm release metadata without a spawn mock
Keep the npm 11 string and npm 12 one-element array accepted by the
cherry-picked lookup, and separate invalid metadata from a failed
registry command.
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Co-authored-by: Dapo Olaomo <penielgold@gmail.com>
Read source digests, FAT tables and embedded headers from one opened source stream before translating native offsets. Preserve native mapping observations through changed, missing, nonregular and access-denied source failures; keep filesystem work outside the Hopper API thread.
Exercise source drift, relocated slices, missing files, permissions and recovery through real Hopper CLI/MCP verification for thin, FAT32 and FAT64 inputs.
* feat(clients): register Grok Build and Grok Bot during setup
Detect both clients and install the local REA MCP registration the same
way setup already handles the other agents. Grok Build edits only the
REA tables in its TOML config and sets startup_timeout_sec to 30. Grok
Bot writes the mcpServers.rea entry into mcp.json. That file is the
registration to add to the signed-in account; setup does not call the
account API.
Filed by Grok.
* fix(clients): clear a disabled Grok Build registration during setup
Grok Build keeps a server suppressed when its name stays in
disabled_mcp_servers, and setup was treating that file as already aligned.
Setup now removes only that name, doctor reports the registration stale until
it is gone, and uninstall keeps comments in an inline table whose only server
was REA. Split the lifecycle suite and reflow the get-started page so static
checks pass.
* fix(verify): check packed Hopper search as literal-only
The package verifier still called a regex probe that main deleted. The
native bridge refuses regex and joins string hits with typed records, so
the restored probe stubs that inventory and the check asserts the literal
matches and the regex refusal. The new README translations also name
Grok Build and Grok Bot.
* fix(clients): stop treating a Grok Bot data directory as registered
Grok Bot stores connectors in the signed-in account and runs them on its
hosted computer. Setup no longer writes mcp.json or reports that file as
aligned. Doctor and setup tell the caller to add the server from the
Grok Bot chat.
* fix(clients): drop multiline Grok disable-list entries
Decode disabled_mcp_servers strings with the document parser so a
multiline basic or literal string that loads as rea is removed.
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Co-authored-by: Grok <eugene.ray@gmail.com>
Co-authored-by: Cursor Agent <cursoragent@cursor.com>
Co-authored-by: morluto <morluto@users.noreply.github.com>
morluto
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