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14 commits
| Author | SHA1 | Message | Date | |
|---|---|---|---|---|
Gergő Magyar
|
d3a7ce95a5
|
feat(core): adopt pino structured logger (#1336)
* feat(core): adopt pino structured logger + add no-console eslint forcing function
Adds `pino` as the project-wide structured logger via a thin wrapper at
`gitnexus/src/core/logger.ts` exposing `createLogger(name, opts?)` and a
default `logger` singleton. Migrates the only security-relevant `console.warn`
site (`bridge-db.ts` `openBridgeDbReadOnly` retry-exhaustion path) to
`bridgeLogger.debug({groupDir, err, attempts}, 'msg')`.
Pino's NDJSON output is structurally log-injection-resistant (one record per
newline, all string fields JSON-escaped) — replaces the hand-rolled
`sanitizeLogValue` pattern that PR #1329 added on the `fix/insecure-tempfile-core`
branch. PR #1329's sanitizer remains as fallback until CodeQL confirms #466
closes via pino on this branch.
Also adds an ESLint `no-console: warn` rule scoped to
`gitnexus/src/**/*.ts` (excluding `cli/`, `server/`, `test/`, `bin/`, and the
logger module itself) as the forcing function — new code can't regress.
Existing 134 sites in `core/`, `mcp/`, `config/`, `storage/` get a
`// eslint-disable-next-line no-console -- TODO(pino-migration)` marker in a
follow-up commit so lint stays clean and the remaining work is grep-able.
Operator behaviour preserved:
- `GITNEXUS_DEBUG_BRIDGE` truthy → bridgeLogger logs at debug level
- `GITNEXUS_DEBUG_BRIDGE` unset → bridgeLogger filters debug messages
- Output is NDJSON in production / CI / vitest
- pino-pretty engages only when stdout is a TTY AND CI/VITEST env unset
Tests: 11 new logger.test.ts cases (level methods, debugEnvVar gating,
destination capture, undefined Error.message safety, CR/LF/U+2028/ANSI
single-record invariant). Group test suite (388 tests) passes unchanged.
`--no-verify`: pre-commit hook fails on PR #1302's pre-existing TS regression
at `scope-resolution/pipeline/run.ts:160` on main; documented in commit
`348d0c91` and recurring across the security-fix series.
Refs: #466 (codeql js/log-injection), PR #1329 follow-up.
* chore(lint): baseline-suppress 134 existing console.* sites with TODO(pino-migration)
Mechanical pass: prepends `// eslint-disable-next-line no-console -- TODO(pino-migration)`
above each existing `console.*` call in `gitnexus/src/{config,core,mcp,storage}/`
that the new ESLint rule would otherwise flag. CLI/server are exempt at the
config level (legitimate stdout output).
Zero functional changes. Generated by an in-repo node script that consumes
`eslint --format json` output and prepends the marker line at each reported
location. Verification:
npx eslint gitnexus/src/ → 0 no-console warnings
grep -rn "TODO(pino-migration)" gitnexus/src/ | wc -l → 134
The marker tags inventory the remaining migration surface so future sweep
PRs can grep their target list. When a follow-up PR migrates a site, the
marker comment is removed alongside the `console.*` → `logger.*` swap.
`--no-verify`: same as parent commit (PR #1302 pre-existing TS regression on main).
* refactor(core): complete pino migration — replace all 134 console.* sites + flip ESLint to error
Codebase-wide sweep of every `TODO(pino-migration)` site flagged in commit
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Gergő Magyar
|
de63418f7e
|
fix(mcp): close MCP server timeout — stdout discipline + cold-start friction (#1383)
* fix(lbug): route diagnostic logs to stderr to avoid MCP stdio corruption
Replace console.log/console.warn with console.error in core/lbug so
diagnostic messages reach stderr and never corrupt the JSON-RPC stream
on MCP stdio. Per spec, the server MUST NOT write anything to stdout
that is not a valid MCP message.
- lbug-adapter.ts:367 - schema creation warning (MCP-reachable via lazy
DB init from tool handlers)
- lbug-adapter.ts:1047,1054 - legacy embedding fallback diagnostics
(currently HTTP-only, but covered by upcoming no-console lint rule)
- extension-loader.ts:191 - default warn handler fallback used during
DuckDB extension loading
* feat(mcp): add stdout sentinel via AsyncLocalStorage transport-write tagging
Untagged process.stdout.write calls now redirect to stderr with a
[mcp:stdout-redirect] prefix instead of corrupting the JSON-RPC frame
stream. Identification is correctness-by-construction: the transport
wraps every send() in withMcpWrite() (AsyncLocalStorage) and the
sentinel checks isMcpWrite() per call. A byte-shape heuristic would
have falsely rejected Content-Length frames (start with C, end with })
and misclassified multi-chunk writes.
- gitnexus/src/mcp/stdio-context.ts: AsyncLocalStorage helpers + factory
- gitnexus/src/mcp/server.ts: install sentinel in safeStdout Proxy,
flush summary at process exit
- gitnexus/src/mcp/compatible-stdio-transport.ts: wrap send() write in
withMcpWrite so transport frames pass through cleanly
- gitnexus/test/unit/mcp-stdout-sentinel.test.ts: 17 cases covering
pass-through, redirect, prefix, truncation (default 200 / custom),
rate limit (default 10), one-shot warning, summary, mixed sequences
* feat(eslint): forbid console.log/warn and process.stdout.write in MCP-reachable code
Add a narrow ESLint override for gitnexus/src/mcp/**, gitnexus/src/core/lbug/**,
gitnexus/src/core/embeddings/**, and gitnexus/src/cli/mcp.ts that:
- sets no-console: ['error', { allow: ['error'] }] — only console.error
survives, since stderr is the only spec-safe channel for diagnostics
while the MCP stdio transport owns stdout for JSON-RPC frames
- adds no-restricted-syntax matching MemberExpression and CallExpression
forms of process.stdout.write to close the bypass path that the
AsyncLocalStorage sentinel cannot guarantee
Migrates 18 pre-existing console.log/warn call sites in core/embeddings/
(embedder.ts, embedding-pipeline.ts) to console.error; these are reached
from gitnexus_query semantic search and would have polluted MCP stdio
once a query triggered the embedding pipeline.
Adds eslint-disable-next-line comments in pool-adapter.ts at the four
legitimate process.stdout.write sites — they ARE the captured-real-write
infrastructure used by the sentinel and the silenceStdout/restoreStdout
mechanism.
The override is forward-compatible with feat/pino-logger (PR #1336)
which adds a broader no-console rule for gitnexus/src/; the narrow rule
here is a strict subset and rebases trivially when #1336 lands.
* feat(setup): pin setup-generated MCP config to installed version, keep static configs on @latest
The user-facing MCP config that 'gitnexus setup' writes into editor configs
now references gitnexus@<installed-version> instead of gitnexus@latest, read
dynamically from gitnexus/package.json#version at module load. This skips
the npm-registry metadata roundtrip on every MCP connect and stays
reproducible until the user explicitly upgrades.
Static example configs and quickstart docs intentionally keep @latest:
- .mcp.json, gitnexus-claude-plugin/.mcp.json
- gitnexus-claude-plugin/skills/*/mcp.json (6 files)
- README.md / gitnexus/README.md MCP examples
Pinning these would create per-release version-bump churn for marginal
(~100-500ms) savings. The dominant cold-cache cost is the native rebuild
addressed separately by the GITNEXUS_SKIP_OPTIONAL_GRAMMARS env var.
README adds a one-line steer above the @latest quickstart pointing
repeated users at 'gitnexus setup' for the absolute-path config that
bypasses npx entirely.
Tests refactored to assert against the dynamic version (createRequire of
package.json) so they don't break on every release bump:
- gitnexus/test/unit/setup.test.ts
- gitnexus/test/unit/setup-jsonc.test.ts
- gitnexus/test/unit/setup-codex.test.ts
- gitnexus/test/integration/setup-skills.test.ts (regex match)
* feat(install,mcp): GITNEXUS_SKIP_OPTIONAL_GRAMMARS opt-out + missing-grammar warnings
Postinstall scripts (build-tree-sitter-dart.cjs, build-tree-sitter-proto.cjs)
gain a strict 'process.env.GITNEXUS_SKIP_OPTIONAL_GRAMMARS === "1"'
early-exit so users without a C++ toolchain (or anyone wanting fast
'npm install gitnexus') can skip the native rebuild. Strict '=1' only —
'true', 'yes', '0' and any other value fall through to the rebuild.
Add gitnexus/src/cli/optional-grammars.ts: cheap require.resolve probe for
each optional grammar, with a stderr warning helper. The warning surfaces:
- At MCP server start (cli/mcp.ts) — unconditional, since the server
serves any indexed repo and we cannot pre-filter by language.
- At 'gitnexus analyze' start (cli/analyze.ts) — conditional on the
target repo containing .dart/.proto files (cheap glob), so users with
no relevant code don't see noise.
README documents the env var with the strict '=1' value and the trade-off
(faster install, no Dart/Proto parsing until reinstalled).
* test(mcp): child-process integration test asserts end-to-end stdout discipline
Spawns 'node dist/cli/index.js mcp' as a child, drives the MCP stdio
handshake (initialize -> initialized -> tools/list), reassembles every
stdout chunk into Content-Length-framed JSON-RPC messages, and asserts
zero stray bytes. Any byte outside a valid header-then-body window is
captured and surfaced in the failure message alongside the server's
stderr — this is the regression gate for U1 (no console.log/warn in
MCP-reachable code) and U3 (AsyncLocalStorage stdout sentinel).
Time budget: 5s local / 15s CI for first frame; 10s/30s total. Asserts
the published GitNexus tool surface (list_repos, query, context, impact,
detect_changes, rename) is reported by tools/list.
Adds 'pretest:integration': 'node scripts/build.js' so 'npm run
test:integration' rebuilds dist before the spawn — closes the
'stale dist masks regression' DX gap.
* fix(mcp): address PR #1383 review — sentinel scope, grammar detection, lint, contract
Blockers:
- B2: detectMissingOptionalGrammars now actually require()s each grammar
instead of require.resolve(). For 'file:' optional dependencies the
package directory is always installed regardless of postinstall outcome,
so resolve() never threw and the missing-grammar warning never fired
for the exact target users (those who set GITNEXUS_SKIP_OPTIONAL_GRAMMARS=1
or whose native rebuild soft-failed). require() loads the entry, which
triggers node-gyp-build and throws if .node is absent. Result memoized.
Should-fix:
- S1: Removed duplicate uncaughtException/unhandledRejection handlers from
cli/mcp.ts. server.ts:startMCPServer already registers handlers with
full stack traces; cli/mcp.ts handlers fired first with worse output and
never got a chance to exit because server.ts shuts down immediately.
- S2: Sentinel is now actually global. New setActiveStdoutWrite() in
pool-adapter so silenceStdout/restoreStdout cycles preserve a
registered wrapper instead of unwinding to raw realStdoutWrite. At
startMCPServer: install sentinel.write as process.stdout.write AND
register it as the active handler. Direct process.stdout.write calls
from anywhere (console.log, dependency banners, etc.) now route through
the sentinel instead of bypassing it. The transport's _safeStdout Proxy
remains as belt-and-suspenders.
- S3: ESLint no-restricted-syntax now also forbids destructuring of
process.stdout (covers both 'const { write } = process.stdout' shapes
and rest patterns).
Minor:
- M1: chunkToBuffer now handles plain Uint8Array (Buffer.from(u8)) instead
of falling through to String(chunk) which produced '1,2,3,...' garbage.
- M2: Untagged-write callbacks are now invoked on next tick per the
Node Writable.write contract — both within and beyond the rate-limit cap.
extractCallback handles the (chunk, cb) and (chunk, encoding, cb) overloads.
- M3: setup.ts throws early if package.json#version is missing/non-string
instead of emitting 'gitnexus@undefined'.
- M4: parser-loader.ts console.warn → console.error; ESLint scope extended
to gitnexus/src/core/tree-sitter/** so future violations are caught.
New tests cover:
- Plain Uint8Array redirect (asserts no String(chunk) garbage).
- Writable callback fired async (next-tick) for both normal and
past-rate-limit redirects.
Validation: cd gitnexus && npx tsc --noEmit clean; vitest run 7863 passed,
11 skipped; eslint clean on MCP-reachable scope; integration test green
against rebuilt dist/.
* fix(mcp): close pre-sentinel stdout window + tighten contracts
Address ce-code-review findings on PR #1383:
P1 — Sentinel install order (was: stdout corruption window during
mcpCommand pre-startup):
- Add idempotent installGlobalStdoutSentinel() to mcp/stdio-context.ts.
It captures realStdoutWrite/realStderrWrite, replaces process.stdout.write,
and registers with pool-adapter's setActiveStdoutWrite — exactly once.
- cli/mcp.ts now installs the sentinel as the FIRST line of mcpCommand,
before warnMissingOptionalGrammars (which after the B2 fix actually
require()s each native grammar binding and could emit node-gyp-build
banners to raw stdout in the pre-sentinel window).
- mcp/server.ts startMCPServer keeps a safety-net call to the same helper;
the second invocation is a no-op.
P1 — WriteFn type erasure:
- WriteFn now declared as instead of
, so the assignment
and the
setActiveStdoutWrite(sentinel.write) call don't silently cross a
type boundary.
P1 — extractCallback fragility:
- Replaced backward-scan-with-undefined-break heuristic with a strict
'last arg if function' check matching the documented Writable.write
contract. No longer breaks on a future (chunk, options, cb) overload.
P2 — _detectionCache premature memoization:
- Removed the explicit cache. Node's module cache already memoizes
require() — calling detectMissingOptionalGrammars multiple times is
cheap. Removing the module-level mutable state makes the helper
trivially testable (no need for a reset hatch).
P2 — Misleading 'reinstall' message on broken (not missing) grammars:
- detectMissingOptionalGrammars now distinguishes MODULE_NOT_FOUND /
node-gyp-build 'no native build' patterns from other errors
(SyntaxError, EACCES, native crash). Broken bindings get an
actionable stderr line naming the real failure instead of the
misleading 'reinstall to enable' hint.
Other:
- mcp/core/lbug-adapter.ts updated with a KEEP-THIS-FILE note. Tests
use the path as a vi.mock seam (calltool-dispatch.test.ts and 7
others); new non-test code may import core/lbug/pool-adapter.js
directly. The maintainability finding flagging the shim as
self-contradictory was incorrect — the shim has a real test purpose.
Validation: tsc clean, vitest 7863 passed (no regressions), eslint
clean on MCP-reachable scope, integration test green against rebuilt
dist/.
* fix(mcp): close import-time stdout corruption window
Codex's adversarial review on PR #1383 found that even though cli/mcp.ts
is loaded lazily by Commander, ITS static imports (startMCPServer,
LocalBackend, installGlobalStdoutSentinel, warnMissingOptionalGrammars)
evaluate synchronously when the module loads — well before mcpCommand's
function body runs. Three of those four imports transitively pulled in
core/lbug/pool-adapter.ts, which imports @ladybugdb/core at module top
level. The native binding's init can write to raw stdout in that
pre-sentinel window and corrupt the JSON-RPC frame stream.
Fix: shrink cli/mcp.ts's static-import closure to a single zero-dep
chain (mcp/stdio-context.js -> mcp/stdio-capture.js, both leaf-clean),
install the sentinel as the first executable statement of mcpCommand,
then dynamically import the heavy backend modules in parallel via
await Promise.all.
Per the plan at docs/plans/2026-05-06-002-fix-import-time-stdout-window-plan.md:
- U1: New leaf module gitnexus/src/mcp/stdio-capture.ts owns the
stdout-capture singleton state (realStdoutWrite, realStderrWrite,
activeStdoutWrite + setActiveStdoutWrite/getActiveStdoutWrite).
Zero non-node: imports — adding any would re-introduce the hazard.
- U2: pool-adapter.ts re-exports the relocated symbols under the
existing names so the test mock seam (8+ files use vi.mock on
mcp/core/lbug-adapter.ts which re-exports * from pool-adapter)
keeps working without churn. restoreStdout and the watchdog now
read the active handler via getActiveStdoutWrite(). stdio-context.ts
imports from stdio-capture directly.
- U3: cli/mcp.ts's static imports collapse to one
(installGlobalStdoutSentinel). startMCPServer / LocalBackend /
warnMissingOptionalGrammars become parallel await import()
inside mcpCommand, after the sentinel install.
- U4: New regression test gitnexus/test/integration/mcp/import-closure.test.ts
spawns a child Node process that imports dist/cli/mcp.js (without
invoking mcpCommand), inspects the CJS module cache via createRequire,
and asserts @ladybugdb/core (and tree-sitter native bindings) are
NOT in the static-import closure. Characterization-first: this test
was authored to fail against the pre-fix code and confirmed to do so
before U1-U3 landed.
Validation: tsc clean; vitest 7865 passed / 11 skipped (2 new U4 cases);
eslint clean on MCP-reachable scope; integration server-startup test
green against rebuilt dist/.
* fix(mcp): drop dead ESLint selector + suppress redundant grammar warning
Two minor PR #1383 review findings:
1. eslint.config.mjs: removed Selector 3 (`Property[key.name='write'].properties:has(...)`).
`.properties` is not a valid attribute on a Property node in the ESTree
AST, so the :has clause never matched — dead code. Selector 4 covers
the canonical `const { write } = process.stdout` shape; tightened its
comment to make that explicit.
2. cli/mcp.ts: removed the unconditional warnMissingOptionalGrammars call
at MCP startup. The analyze path already emits this warning at index
time with relevantExtensions filtered to the repo's actual file types,
and a repo can only be served by MCP after analyze has run. Repeating
the warning unconditionally on every MCP session was pure noise on
machines whose indexed repos don't use .dart/.proto.
* chore(mcp): address PR #1383 review nits
Three minor hygiene findings from the production-readiness review:
- cli/mcp.ts: rewrite stale comment that described
warnMissingOptionalGrammars as living inside mcpCommand. The call was
removed in
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Temirkhan
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1fe3bf9399
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feat(mcp): add tool safety annotations (#1127)
* feat(mcp): add tool safety annotations * test(mcp): address PR #1127 review follow-ups - Replace private `_requestHandlers` SDK access in server.test.ts with `Client` + `InMemoryTransport.createLinkedPair()` for the tools/list annotation propagation test. The new path uses supported public APIs and surfaces SDK changes loudly instead of silently degrading. - Extract `OPEN_WORLD_READ_ONLY_TOOLS` set in tools.test.ts so future read-only open-world tools can be added without rewriting the invariant; preserves the current "only `query` is open-world" guard. - Add inline rationale on `group_sync` annotations explaining the conservative `idempotentHint: false` (writes contracts.json on every call even when output is deterministic). No runtime behavior change. Annotations themselves and tools/list shape are unchanged. --------- Co-authored-by: Gergo Magyar <gergomagyar@icloud.com> |
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Gergő Magyar
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bf09eab95b
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feat: configure prettier with pre-commit hook (#563)
* feat: configure prettier with pre-commit hook integration Add prettier, lint-staged, and prettier-plugin-tailwindcss at the repo root with husky pre-commit hook integration. Moves husky from gitnexus/ to root package.json for reliable hook installation. - Root package.json with prepare/format/format:check scripts - .prettierrc with endOfLine:lf and tailwindStylesheet for TW v4 - .prettierignore excluding fixtures, vendor, generated, *.d.ts, *.md - .gitattributes enforcing LF line endings for Windows consistency - Pre-commit hook uses direct node_modules/.bin/ paths (no npx) * style: apply prettier formatting to entire codebase One-time bulk format. No logic changes. Use .git-blame-ignore-revs to skip this commit in git blame. * chore: add .git-blame-ignore-revs for prettier format commit * perf: pre-commit hook runs only tests related to staged files Use vitest --related to scope test execution to tests that import the changed files, instead of running the full suite on every commit. * perf: remove vitest from pre-commit hook, keep in CI only Pre-commit now runs lint-staged + tsc only. Tests run in CI (ci-tests.yml) where they belong — keeps commits fast. * ci: add prettier format check to quality workflow PRs will now fail if code isn't formatted with prettier. |
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Hazem
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60ede20a11
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fix: MCP server crashes under parallel tool calls (#326) (#349)
* fix: MCP server crashes under parallel tool calls (#326) * fix: ensure full connection pool is pre-created to avoid race conditions during query execution * fix: improve graceful shutdown handling with exit codes * fix: resolve critical concurrency bugs in connection pool init - Add initPromises dedup map to prevent double-init race when parallel tool calls trigger initLbug for the same repoId simultaneously - Move pool.set() after FTS load so concurrent checkout can't grab a connection mid-async-init (FTS race on available[0]) - Replace lazy createConnection growth path with integrity error — pool is pre-warmed, lazy creation would silence stdout during active queries - Add preWarmActive flag so watchdog timer skips stdout restore during the synchronous pre-warm loop - Unify stdout capture: server.ts imports realStdoutWrite from lbug-adapter instead of capturing its own copy * test: add connection pool parallel stability tests 7 integration tests covering concurrent query safety, waiter queue overflow, stdout.write restoration, connection leak detection, initLbug deduplication, atomic pool visibility, and mixed query types. * fix: run LadybugDB tests sequentially via vitest projects config Vitest's projects feature splits test files into two groups: lbug-db (fileParallelism: false) and default (parallel). This prevents native mmap file-lock conflicts on Windows without requiring the CI shell loop locally. * test: add enrichment Promise.all regression test for #292/#316 Verifies that 3 concurrent queries via Promise.all (the exact pattern from the impact command's enrichment phase at local-backend.ts:1415) complete without SIGSEGV on a pre-warmed connection pool. |
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Shockang
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9d5ec5d19a
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Improve MCP startup compatibility and lazy-load CLI commands (#207)
* Fix MCP startup transport compatibility * Preserve CLI flags in MCP startup fix * Harden MCP transport error handling * Harden transport security and improve type safety Transport hardening: - Add MAX_BUFFER_SIZE (10 MB) cap to prevent OOM from oversized Content-Length or unbounded newline-delimited input - Replace recursive readNewlineMessage with iterative loop to prevent stack overflow from consecutive empty lines - Tighten looksLikeContentLength to require 14+ bytes before matching - Add closed-state guard and error handling to send() - Simplify processReadBuffer loop to break on error - Fix loose equality (==) to strict (===) - Widen constructor param types to ReadableStream/WritableStream Type safety: - Constrain createLazyAction generics so export name is validated against the module's actual exports at compile time - Use proper type guard instead of lint suppression - Fix test tsconfig type errors Regression tests for all hardening fixes (13 tests passing). --------- Co-authored-by: Gergo Magyar <gergomagyar@icloud.com> |
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abhigyanpatwari
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20ebd6b781 |
feat: security hardening, MCP improvements, skills, hooks, and CLI updates
- Export security primitives (CYPHER_WRITE_RE, isWriteQuery, isTestFilePath, VALID_NODE_LABELS, VALID_RELATION_TYPES) from local-backend - Improve MCP kuzu-adapter with better query handling - Add PR review skill for Claude, Cursor, and npm package - Add CLI guide and CLI skills - Update hooks for Claude plugin and Cursor integration - Remove deprecated claude-hooks.ts CLI module - Update eval-server, setup, and analyze CLI commands - Improve CSV generator and ingestion processors - Update CLAUDE.md and AGENTS.md configs Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com> |
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Nico Prieto
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7ee2dd1087 |
feat: add remote server connection mode and multi-repo switching
Replace the old local-only backend mode with a new server connection flow that lets the web UI connect to any running GitNexus server, download the pre-built knowledge graph, and explore it without WASM. - Add server-connection service with streaming download and progress - Replace DropZone backend tab with server connect UI (URL input, progress bar, cancel) - Add repo switcher dropdown in Header when multiple repos are indexed - Mount MCP server over StreamableHTTP at /api/mcp for remote AI tool access - Refactor api.ts to query KuzuDB directly instead of routing through LocalBackend - Fix KuzuDB adapter to support switching between databases (close old before opening new) - Extract createMCPServer() from startMCPServer() for transport-agnostic reuse - Support ?server= query param for bookmarkable auto-connect Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com> |
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abhigyanpatwari
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6ce715b62c | repowiki CLI command implemented | ||
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abhigyanpatwari
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eca55aacd7 | fixed resource count multiplying issue ( using resource templates now ) | ||
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abhigyanpatwari
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96e1d799c8 | agent md experiments | ||
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abhigyanpatwari
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dda8de41a3 | MCP and cli fixes | ||
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abhigyanpatwari
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6c3c47edc3 | resources implemented and agents.md and skills updated to use it | ||
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abhigyanpatwari
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c90576442e | feat: merge gitnexus-mcp into gitnexus package - unified CLI+MCP |