Release v1.3.1

Changelog

All notable changes to Code-Index-MCP will be documented in this file.

The format is based on Keep a Changelog,
and this project adheres to Semantic Versioning.

[Unreleased]

[Unreleased]: # placeholder for post-rc5 work

[1.3.1] — 2026-07-10 (Unpublished)

Fixed

• Enforced the FastAPI JWT boundary independently from the optional local
  STDIO handshake and removed ambiguous repository-selector fallback.
• Made staged index recovery atomic and fail closed, unified summarization
  results, and bounded sandbox worker lifecycle and request handling.
• Restored deterministic local quality gates, release-critical typing, and
  hermetic test execution across the supported release matrix.
• Split release preparation from protected-main publication and pinned every
  external GitHub Action to an immutable upstream commit.

Release status

• Package, runtime, active documentation, installers, and local build artifacts
  are prepared as 1.3.1 / v1.3.1.
• No tag, GitHub release, container image, attestation, or PyPI package was
  published by this hardening phase.

[1.3.0] — 2026-07-06

Added

• Added the public mcp_server.client Python API with typed local search,
  symbol lookup, reindex, and status operations for programmatic use without
  starting MCP STDIO or FastAPI.
• Added source metadata filters for ordinary code, friction signals, and
  historical GitHub issue context across the direct client, MCP tool handlers,
  and FastAPI /search.

Changed

• Advanced the repo-owned package, runtime, release automation, installer, and
  active public documentation surface from 1.2.0 / v1.2.0 to 1.3.0 /
  v1.3.0.
• Preserved index-it-mcp as the canonical Python distribution while keeping
  code-index-mcp limited to repository, client-local server, and container
  naming surfaces.

[1.2.0] — 2026-04-25

Changed (GAREL — stable surface preparation)

• Prepared the stable 1.2.0 / v1.2.0 repo-owned release surface across
  package metadata, runtime metadata, release automation defaults, active
  install docs, support docs, and Docker installer helpers.
• Preserved v1.2.0-rc8 as historical prerelease soak evidence only while
  routing the actual stable dispatch and GA release evidence to downstream
  GADISP.

Known limitations

• This phase did not dispatch the stable release; GitHub Latest and Docker
  latest remain stable-only outputs that are still verified in GADISP.
• Beta, experimental, unsupported, and disabled-by-default support-tier limits
  remain governed by docs/SUPPORT_MATRIX.md; stable surface prep does not
  broaden product topology or runtime claims.

[1.2.0-rc8] — 2026-04-25

Changed (GARECUT — post-remediation RC recut freeze)

• Advanced the active remediated RC recut contract to 1.2.0-rc8 /
  v1.2.0-rc8 across package metadata, runtime metadata, release automation
  defaults, and installer helpers without widening into GA channel changes.
• Froze the rc8 recut evidence and final-decision handoff expectations so a
  blocked or successful prerelease proof can route the next work either back
  through renewed GAREL or into a GARECUT rerun without silently authorizing
  GA.

Known limitations

• v1.2.0-rc8 remains a prerelease RC/public-alpha or beta channel artifact;
• it does not authorize GA wording, GitHub Latest promotion, or stable Docker
  latest; GitHub Latest is not the RC policy source.
• GARECUT dispatch still requires a clean enough release worktree, HEAD == origin/main, and unused local plus remote v1.2.0-rc8 tags before
  gh workflow run may execute.

[1.2.0-rc7] — 2026-04-24

[1.2.0-rc6] — 2026-04-24

Changed (GARC — follow-up RC soak freeze)

• Advanced the active follow-up RC contract to 1.2.0-rc6 / v1.2.0-rc6
  across package metadata, runtime metadata, release automation defaults,
  installer helpers, README status, and the active Docker/MCP configuration
  docs.
• Added explicit follow-up RC soak operator guidance and evidence reduction for
  GARC so dispatch prerequisites, workflow observation fields, and blocked-stop
  handling are frozen before any new release mutation.

Known limitations

• v1.2.0-rc6 remains a prerelease RC/public-alpha or beta channel artifact;
  it does not authorize GA wording, GitHub Latest promotion, or stable Docker
  latest; GitHub Latest is not the RC policy source.
• GARC dispatch still requires a clean worktree plus fresh upstream
  governance/E2E/operations evidence before gh workflow run may execute.

[1.2.0-rc5] — 2026-04-23

Fixed (P27-P33 — v3 multi-repo blocker closeout)

• Added fail-closed readiness handling for missing, empty, stale, building,
  wrong-branch, and unsupported-worktree indexes. Query tools now return
  index_unavailable with safe_fallback: "native_search" instead of
  dispatching against an unsafe index.
• Hardened the v3 repository model around many unrelated repositories on one
  machine, one registered worktree per git common directory, and tracked/default
  branch indexing only.
• Added the P33 production multi-repo matrix for unrelated repo isolation,
  same-repo worktree rejection, wrong-branch safety, stale/missing index
  fallback, incremental repair, rename/delete/revert, force-push recovery, and
  wrong-artifact rejection.

Changed (P34 — public alpha recut)

• Recut the public-alpha release contract to 1.2.0-rc5 / v1.2.0-rc5 across
  package metadata, runtime metadata, release automation, README status,
  Docker/MCP setup docs, and docs/SUPPORT_MATRIX.md.
• Aligned outside-developer docs, operator runbooks, and agent handoffs on the
  readiness contract: indexed MCP results are authoritative only when readiness
  is ready; otherwise users should use native search or follow the returned
  remediation.
• Updated docs/operations/deployment-runbook.md to require P27-P33 gates,
  make alpha-production-matrix, docs truth tests, release metadata tests, and
  clean-checkout wheel/container smoke before public-alpha promotion.

Known limitations

• Same-repo sibling worktrees and non-default branch queries are not independent
  indexed-search contexts in v3; they return index_unavailable with
  safe_fallback: "native_search" until a future release expands the topology
  contract.
• Language/runtime support remains scoped by docs/SUPPORT_MATRIX.md, release
  promotion remains gated by docs/operations/deployment-runbook.md, and the
  public-alpha go/no-go evidence remains linked from
  docs/validation/private-alpha-decision.md.

[1.2.0-rc4] — 2026-04-22

Added (P26 — private alpha evidence and public alpha decision)

• Added the P26 private-alpha evidence contract:
  docs/validation/private-alpha-decision.md,
  docs/validation/private-alpha-evidence.schema.json, and the ignored
  private-alpha-evidence/ raw-output boundary.
• Added scripts/private_alpha_evidence.py for local private fixture runs across
  python_repo, typescript_js_repo, mixed_docs_code_repo,
  multi_repo_workspace, and large_ignored_vendor_repo before public alpha.
• Documented public-alpha release truth: supported install paths are
  uv sync --locked/STDIO and ghcr.io/viperjuice/code-index-mcp; language
  support is scoped by docs/SUPPORT_MATRIX.md; beta warnings and rollback
  instructions remain in docs/operations/deployment-runbook.md.

[1.2.0-rc3] — 2026-04-21

Changed (P21 — release contract and dependency unification)

• Unified the P21 release contract across runtime metadata, package metadata,
  README status, changelog, and release automation around 1.2.0-rc3.
• Removed active workflow and Docker dependency references to retired
  requirements*.txt inputs in favor of the locked pyproject.toml/uv.lock
  dependency source.
• Expanded release metadata and requirements-consolidation tests to guard the
  P21 contract surfaces consumed by P22.

Added (P25 — blocking release gates and automation)

• Added explicit public alpha gate jobs for dependency sync, focused format/lint,
  unit plus release smoke, integration smoke, Docker build/smoke, docs truth, and
  required-gate aggregation.
• Added release automation preflight refusal before version mutation, release
  branch creation, artifact build, tag creation, GitHub release creation, PyPI
  publish, or container publish.
• Documented the operator gate checklist and private-alpha authenticated
  attestation fallback for missing ATTESTATION_GH_TOKEN or repository
  attestation settings.

[1.2.0-rc2] — 2026-04-20

Fixed (P20 — sandbox/OpenBLAS hotfix, observability bugs)

• (P20 SL-0) Raised CapabilitySet.mem_mb default from 512 to 2048
  so sandbox-default-on plugins that transitively import numpy/OpenBLAS
  no longer abort on RLIMIT_AS. Closes IF-0-P20-3.
• (P20 SL-2b) Prometheus /metrics endpoint now exposes
  mcp_tool_calls_total, mcp_rate_limit_sleeps_total, and
  mcp_artifact_errors_by_class_total. Previously a registry split
  meant the counters lived on the default REGISTRY while the exporter
  served a private one.
• (P20 SL-2b) SecretRedactionResponseMiddleware is now applied
  on subprocess uvicorn boot. Previously it was registered in a startup
  hook that ran after FastAPI sealed its middleware stack, so subprocess
  gateways never redacted Bearer ... tokens in HTTP responses.

Added (P20 — validation harness, runbook, observability smoke)

• (P20 SL-1) New tests/integration/multi_repo/ harness — pytest
  fixture spawns ≥2 live uvicorn gateway subprocesses sharing one
  registry; tests cover concurrency (200 entries), cross-repo delta
  resolution, and dispatcher repo_id isolation. Closes IF-0-P20-1.
• (P20 SL-2) New tests/integration/obs/ smoke — docker-compose
  Prom+Loki stack proves JSON log parse rate, counter scrape, and
  secret redaction over HTTP. Skips cleanly without docker.
• (P20 SL-3) New docs/operations/deployment-runbook.md with
  measurable bake-pass criteria, bake windows, and rollback procedures
  per stage (dev/staging/canary/full-prod). Closes IF-0-P20-2.

[1.2.0-rc1] — 2026-04-20

Added (P18 — Enforcement, Artifact Resilience & Ops)

• Route auth enforcement (IF-0-P18-4): validate_production_config() body fills weak-JWT, CORS-wildcard, permissive rate-limit, and weak-admin-password checks. render_validation_errors_to_stderr() emits [FATAL]/[WARN]-prefixed listings. Gateway startup exits non-zero on any fatal validation error in production; WARN-continues in dev/test. Auth added to /search/capabilities, /graph/context, /graph/search. (mcp_server/gateway.py, mcp_server/config/validation.py, tests/security/test_route_auth_coverage.py, tests/security/test_startup_config_validation.py)
• Artifact pipeline resilience: publisher try/finally rollback via gh release delete on downstream failure; artifact_download delta-base-missing fallback to full artifact; _respect_rate_limit parses Retry-After (int-seconds or HTTP-date, capped 300s) and distinguishes 403 (TerminalArtifactError) from 429 (backoff + retry); attestation preflight checks attestations:write scope. (mcp_server/artifacts/publisher.py, artifact_download.py, providers/github_actions.py, attestation.py)
• Retention janitor CLI (IF-0-P18-2): python -m mcp_server.cli retention prune --repo OWNER/REPO [--dry-run] [--older-than-days N] [--keep-latest-n N]. Protects index-latest and isLatest=true releases. New mcp_server/artifacts/retention.py policy module; new mcp_server/cli/retention_commands.py click group.
• JSON logging: hand-rolled JSONFormatter in mcp_server/core/logging.py; emits {"timestamp","level","name","message", ...extras}. Gated on MCP_ENVIRONMENT=production or MCP_LOG_FORMAT=json.
• Secret redaction middleware (IF-0-P18-1): SecretRedactionResponseMiddleware rewrites Bearer \S+, JWT_SECRET_KEY=\S+, GITHUB_TOKEN=\S+ to [REDACTED] in 4xx/5xx response bodies. Streaming bodies pass through unmodified (documented limitation). (mcp_server/security/security_middleware.py)
• Prometheus counters: mcp_rate_limit_sleeps_total (no labels) and mcp_artifact_errors_by_class_total{error_class}. Scrapeable on /metrics. (mcp_server/metrics/prometheus_exporter.py)
• Attestation boot probe: probe_gh_attestation_support() (lru_cache'd) runs gh attestation --help. Boot banner emits ATTESTATION_PREREQ WARN if the subcommand is unavailable and MCP_ATTESTATION_MODE=enforce. (mcp_server/artifacts/attestation.py, mcp_server/cli/stdio_runner.py)
• stdio_runner module surface (IF-0-P18-3): initialize_services() and call_tool(name, arguments) hoisted from _serve() closures to top-level async functions. Seven runtime state variables (dispatcher, plugin_manager, sqlite_store, initialization_error, _file_watcher, _indexing_thread, _fts_rebuild_thread) promoted to module globals. Restores the pre-P2B test surface on the post-P2B file layout. (mcp_server/cli/stdio_runner.py)

Changed (P18)

• Plugin sandbox default (behavioural change): MCP_PLUGIN_SANDBOX_ENABLED=1 is no longer required — sandboxing is now ON by default. Set MCP_PLUGIN_SANDBOX_DISABLE=1 to opt out. See docs/security/sandbox.md for migration notes. (mcp_server/plugins/plugin_factory.py)

Fixed (P18 — P17 straggler burn-down)

• Full-suite failure count closed from 19 (P17 SL-4b close) to 4. The 17 tests/test_mcp_server_cli.py failures and 2 tests/test_benchmarks.py SLO failures now pass; residual 4 are pre-existing integration tests gated on gh CLI attestations:write scope and an unrelated P16 vocabulary signature mismatch. (mcp_server/cli/stdio_runner.py, mcp_server/benchmarks/benchmark_suite.py, mcp_server/plugins/sandboxed_plugin.py)

Added (P17 — Durability & Multi-Instance Safety)

• Registry flock protocol (IF-0-P17-1): RepositoryRegistry.save() acquires
  fcntl.flock(LOCK_EX) on a sibling .lock file, then performs a read-merge-write
  with an atomic rename(). Two concurrent processes calling save() against the same
  file no longer lose each other's writes. (mcp_server/storage/repository_registry.py,
  tests/test_registry_concurrency.py)
• Singleton reset wired: reset_process_singletons() (P16 IF-0-P16-4 stub) is now
  called at the top of initialize_stateless_services(). Repeat-init in the same
  Python process yields fresh managers. (mcp_server/cli/bootstrap.py,
  tests/test_singleton_reset.py)
• Ref-poller edge-case handling (SL-2): RefPoller detects detached HEAD,
  force-push, and branch-rename; each triggers enqueue_full_rescan(repo_id) to prevent
  incremental indexing on a rewritten history. (mcp_server/watcher/ref_poller.py,
  tests/test_ref_poller_edges.py)
• Sweeper observability (SL-2): WatcherSweeper exceptions emit WARNING log and
  increment mcp_watcher_sweep_errors_total Prometheus counter.
  (mcp_server/watcher/sweeper.py, tests/test_sweeper_observability.py)
• MCP_MAX_FILE_SIZE_BYTES enforced (SL-2): Dispatcher walker (index_directory)
  now skips files larger than MCP_MAX_FILE_SIZE_BYTES (default 10 MiB); oversize
  files are logged and skipped without stalling the indexer.
  (mcp_server/dispatcher/dispatcher_enhanced.py)
• Checkpoint clears on clean exit (SL-2): IncrementalIndexer clears the
  checkpoint file even when errors is non-empty on clean exit; a re-run starts fresh
  rather than resuming from a stale error state.
  (mcp_server/indexing/incremental_indexer.py)
• ENOSPC → read-only store (SL-3): SQLiteStore catches OSError(ENOSPC) on
  commit(), transitions to read-only mode, and increments
  mcp_storage_readonly_total. The server keeps serving reads without crashing.
  (mcp_server/storage/sqlite_store.py, tests/test_disk_full.py)
• Schema migration backup (SL-3): SchemaMigrator.migrate_artifact() writes a
  timestamped .backup copy of the DB before any migration; rollback-on-failure
  restores from backup. (mcp_server/storage/schema_migrator.py,
  tests/test_schema_migration_backup.py)
• UnknownSchemaVersionError in core/errors.py (SL-3): UnknownSchemaVersionError
  promoted from schema_migrator.py to mcp_server/core/errors.py, extending the P16
  IF-0-P16-1 taxonomy by one class.
• RerankerFactory.create_default() (SL-4): RerankerFactory.create_default()
  returns a functional reranker; resolves the P14 carry-over.
  (mcp_server/plugins/reranker_factory.py)
• Ruff F401 clean (SL-4): ruff F401 count across mcp_server/dispatcher,
  mcp_server/storage, mcp_server/watcher is 0.
• Multi-instance runbook (SL-docs): docs/operations/multi-instance.md — flock
  protocol, singleton-reset semantics, DR/recovery procedure.
• Vocabulary freeze (IF-0-P17-1): Registry flock + read-merge-write pattern is
  frozen as a named interface for cross-phase reference.
• Test-debt ledger (SL-docs): docs/operations/known-test-debt.md enumerates
  residual failures after P17 close (56 total; 9 cross-repo coordinator carry-over +
  47 pre-existing in other modules).

Added (P16 — Shared Vocabulary Preamble)

• Frozen error taxonomy (IF-0-P16-1): New error classes TransientArtifactError, TerminalArtifactError, and SchemaMigrationError in mcp_server/core/errors.py for structured error handling in artifact operations. Stubs only — no consumer wiring.
• Lazy env-var getters (IF-0-P16-2): Five new environment variable getters in mcp_server/config/env_vars.py — get_max_file_size_bytes(), get_artifact_retention_count(), get_artifact_retention_days(), get_disk_readonly_threshold_mb(), and get_publish_rollback_enabled() — with sensible defaults. Stubs only — no consumer wiring.
• ValidationError dataclass + validate_production_config (IF-0-P16-3): New ValidationError dataclass and keyword-only validate_production_config(environment: str = "production") function in mcp_server/config/validation.py. Stubs only — no consumer wiring.
• reset_process_singletons (IF-0-P16-4): New utility function in mcp_server/cli/bootstrap.py for test isolation and graceful restarts. Stubs only — no consumer wiring.

Added (P15 — Security Hardening)

• Plugin sandboxing (IF-0-P15-1): Plugins execute in isolated worker processes with JSON-line IPC, 30s timeout, and capability-based restrictions. New mcp_server/sandbox/ package with supervisor and adapter; SandboxedPlugin wraps instances with CapabilitySet (filesystem, network, subprocess, env_read). (mcp_server/sandbox/supervisor.py, mcp_server/plugins/sandboxed_plugin.py, tests/security/test_plugin_sandbox.py)
• Metrics endpoint auth (IF-0-P15-2): /metrics requires Authorization: Bearer <token> (app-level) or NetworkPolicy restriction (k8s-only). Wired via require_auth("metrics") middleware. (mcp_server/security/security_middleware.py, mcp_server/api/gateway.py)
• Artifact attestation (IF-0-P15-3): Published artifacts are signed with gh attestation sign and verified with gh attestation verify (requires GITHUB_TOKEN with attestations:write scope). Mode controlled by MCP_ATTESTATION_MODE (enforce/warn/skip). (mcp_server/artifacts/attestation.py, mcp_server/artifacts/publisher.py, mcp_server/artifacts/artifact_download.py)
• Path traversal guard + token validator (IF-0-P15-4): Search results filtered through PathTraversalGuard.normalize_and_check(path, allowed_roots) (controlled by MCP_ALLOWED_ROOTS env). Startup validates GITHUB_TOKEN for all five required scopes via TokenValidator.validate_scopes() (soft-fail default; hard-fail with MCP_REQUIRE_TOKEN_SCOPES=1). Rate-limit backoff on cross-repo artifact fetches. (mcp_server/security/path_guard.py, mcp_server/security/token_validator.py)

Added (P14 — Multi-Repo Completeness + Schema Evolution)

• Reranker wiring (IF-0-P14-1): CrossRepoCoordinator.__init__ now accepts an injected IReranker (mcp_server/indexer/reranker.py); falls back to RerankerFactory.create_default() with graceful degradation to None. (mcp_server/dispatcher/cross_repo_coordinator.py, tests/test_cross_repo_reranker.py)
• Dependency graph (IF-0-P14-2): New mcp_server/dependency_graph/ package with parsers.py, aggregator.py, and ecosystem parsers (Python/npm/Go/Cargo). _get_repository_dependencies returns resolved repo IDs. (mcp_server/dispatcher/cross_repo_coordinator.py)
• Schema migrator (IF-0-P14-3): New mcp_server/storage/schema_migrator.py with SchemaMigrator, UnknownSchemaVersionError, and SchemaMigrationError. Artifact manifests carry schema_version; check_compatibility gates downloads by version. (mcp_server/artifacts/artifact_download.py)
• Auto-delta artifacts (IF-0-P14-4): New mcp_server/artifacts/delta_policy.py with DeltaPolicy/DeltaDecision. Publisher switches to delta mode when artifact exceeds MCP_ARTIFACT_FULL_SIZE_LIMIT (default 500 MB). _get_chunk_ids_for_path accepts limit/offset pagination. (mcp_server/artifacts/publisher.py, mcp_server/artifacts/artifact_upload.py)
• Watcher sweep + rename atomicity (IF-0-P14-5): New mcp_server/watcher/sweeper.py::WatcherSweeper runs full-tree scans every MCP_WATCHER_SWEEP_MINUTES (default 60) to recover dropped inotify/FSEvents events. move_file wrapped in two_phase_commit; raises IndexingError on semantic failure. (mcp_server/dispatcher/dispatcher_enhanced.py, mcp_server/watcher_multi_repo.py)

[1.1.0] - 2026-04-14

Security

• #40 Removed hardcoded JWT_SECRET_KEY and DEFAULT_ADMIN_PASSWORD defaults from
  gateway.py. Server now raises RuntimeError at startup if either env var is unset,
  preventing silent production deployments with known-weak credentials.
  docker-compose.yml and .env.example updated to use env var substitution with no
  insecure literal fallbacks. (mcp_server/gateway.py, docker-compose.yml, .env.example)

Fixed

• #41 get_index_status() symbols_count field now returns the actual number of
  symbols stored for the file (was always 0). Added SQLiteStore.count_symbols_for_file()
  and wired it into IndexEngine.get_index_status().
  (mcp_server/storage/sqlite_store.py, mcp_server/indexer/index_engine.py)
• #41 Reference storage in _store_parse_result() now calls get_symbol() +
  store_reference() instead of silently passing; references are persisted in
  symbol_references and queryable via get_references().
  (mcp_server/indexer/index_engine.py)
• #42 Removed broken curl .../install-mcp.sh line from README (script does not
  exist). Replaced silent TODO in watcher_multi_repo._create_and_upload_artifact() with
  an explicit logger.warning directing users to the CI workflow for artifact upload.
  (README.md, mcp_server/watcher_multi_repo.py)
• Windows CI compatibility: forward-slash path normalization in SQLiteStore.store_file(),
  signal.SIGALRM guard in mcp_server_cli.py, double-quoted git commit messages in
  tests, >= 0 timing assertions for low-resolution Windows clocks.
  (mcp_server/storage/sqlite_store.py, scripts/cli/mcp_server_cli.py,
  tests/test_utilities.py, tests/test_repository_management.py,
  tests/test_multi_repo_search.py, tests/test_dispatcher_advanced.py)
• Benchmark scripts updated to current SQLiteStore/plugin API: replaced removed
  store.add_symbol() with create_repository + store_file + store_symbol, and
  replaced obsolete plugin.extract_symbols() with plugin.indexFile() with
  IndexShard dict-style access.
  (benchmarks/symbol_lookup_benchmark.py, benchmarks/semantic_search_benchmark.py,
  benchmarks/indexing_speed_benchmark.py)

Added

• Backstage catalog registration (catalog-info.yaml) and standard repo layout
  (docs/, mkdocs.yml). (04ea8ff)
• Consiliency maintenance worker trigger workflow for scheduled index health checks.
  (.github/workflows/, 72f15a5)

Added

• Query-intent routing: symbol-pattern queries (class Foo, def bar, CamelCase,
  snake_case) route directly to the symbols table, bypassing BM25. Fixes retrieval for
  class/function lookups that previously returned wrong files.
  (mcp_server/dispatcher/query_intent.py, dispatcher_enhanced.py)
• FlashRankReranker and CrossEncoderReranker (OSS, lazy-loaded); all three rerankers
  share a unified sync interface. Configured via RERANKER_TYPE env var.
  (mcp_server/dispatcher/reranker.py)
• Matrix benchmark: 17-query suite covering all mode × embedding × reranker combinations.
  (scripts/run_matrix_benchmark.py)
• LLM chunk summarization: ChunkWriter / LazyChunkWriter / ComprehensiveChunkWriter;
  per-profile config via summarization: block in code-index-mcp.profiles.yaml.
  (mcp_server/indexing/summarization.py)
• Initial project structure with plugin-based architecture
• FastAPI-based MCP server implementation
• Python plugin with Jedi integration for advanced code analysis
• Tree-sitter wrapper for language parsing
• Semantic indexer with Voyage AI integration
• C4 architecture diagrams using Structurizr DSL
• Comprehensive documentation structure
• Plugin base class for language extensions
• File watcher skeleton for real-time updates
• Cloud sync stub implementation

Changed

• Enhanced Python plugin with proper AST analysis
• Improved error handling in gateway endpoints
• Updated project documentation and README

Added

• MCP InitializeResult.instructions field populated: every connecting client receives
  search-first guidance at handshake time, over any transport (stdio, SSE, HTTP).
  (scripts/cli/mcp_server_cli.py)
• last_indexed field added to search_code results, surfacing the index timestamp so
  agents can assess line-number freshness. (scripts/cli/mcp_server_cli.py,
  mcp_server/storage/sqlite_store.py)
• FileWatcher now auto-starts inside initialize_services() after the dispatcher is
  ready, so the index stays current without any manual setup. Stopped automatically in
  main() finally block on server exit. Only active when using EnhancedDispatcher
  (not BM25-only SimpleDispatcher mode). (scripts/cli/mcp_server_cli.py)
• Auto-index on first run: when no index exists, initialize_services() creates
  .mcp-index/code_index.db and indexes the repository in a background thread. The MCP
  server is immediately responsive; search results populate as indexing progresses.
  Set MCP_AUTO_INDEX=false to disable for large repos and run the reindex tool
  manually. (scripts/cli/mcp_server_cli.py)
• search_code responses now include "indexing_in_progress": true when the initial
  background index is still running, preventing agents from concluding "no results"
  prematurely while the index is being built. (scripts/cli/mcp_server_cli.py)
• FileWatcher start deferred until after background initial index completes, eliminating
  concurrent SQLite write contention between the bulk index_directory() pass and the
  watchdog event handler on first-run repos. (scripts/cli/mcp_server_cli.py)
• .gitignore entries for .mcp-index/code_index.db-shm and .mcp-index/code_index.db-wal
  (SQLite WAL mode sidecar files) added to install.sh and written automatically during
  auto-init so WAL files never appear as untracked. (mcp-index-kit/install.sh,
  scripts/cli/mcp_server_cli.py)
• code-index-mcp.profiles.yaml discovery now searches MCP_PROFILES_PATH env var →
  CWD → server package directory in that order. Previously the file was only found at CWD,
  so semantic profiles silently vanished when cwd was set to another repo. Fallback to the
  server's own installation means semantic search and summarization work out-of-the-box in
  any repo. (mcp_server/config/settings.py)
• ${VAR:default} env-var substitution supported in all base_url fields of
  code-index-mcp.profiles.yaml. Set VLLM_EMBEDDING_BASE_URL or
  VLLM_SUMMARIZATION_BASE_URL to point at any server without editing the YAML.
  (mcp_server/config/settings.py, code-index-mcp.profiles.yaml)
• File-count guard before auto-index: if the target repo exceeds MCP_AUTO_INDEX_MAX_FILES
  (default 100 000), auto-indexing is skipped and a warning is logged. Prevents indefinite
  startup I/O on very large monorepos. (scripts/cli/mcp_server_cli.py)
• BM25 FTS auto-heal: on startup, if an existing index has tracked files but an empty
  fts_code table (e.g. after a migration or partial corruption), a background thread
  calls rebuild_fts_code() automatically. Previously the empty state persisted until
  a manual reindex tool call. (scripts/cli/mcp_server_cli.py)

Fixed

• scripts/cli/mcp_server_cli.py was calling undefined get_settings() on every tool
  invocation, crashing the server before any tool could execute. Replaced with
  Settings.from_environment(). (scripts/cli/mcp_server_cli.py)
• LazyChunkWriter.__init__ was missing the summarization_config parameter despite
  the base class ChunkWriter accepting it, causing a TypeError on every server
  startup. (mcp_server/indexing/summarization.py)
• File watcher trigger_reindex() now calls remove_file() before index_file(),
  preventing stale chunks from persisting when a file edit changes chunk boundaries.
  (mcp_server/watcher.py)
• EnhancedDispatcher.remove_file() now evicts _file_cache before SQLite deletion,
  preventing a skip-on-reindex race where an unchanged-hash file would be left absent
  from the index after a forced removal. (mcp_server/dispatcher/dispatcher_enhanced.py)
• SQLiteStore.remove_file() now deletes symbol_trigrams before symbols, fixing a
  FK constraint failure that silently left file rows in the DB on removal.
  (mcp_server/storage/sqlite_store.py)
• SQLiteStore.remove_file() now clears fts_code entries regardless of whether
  file_id was stored as an integer, absolute path, or relative path string.
  (mcp_server/storage/sqlite_store.py)
• SQLiteStore.search_bm25() now includes last_modified in result rows so the
  last_indexed field is non-null in search results. (mcp_server/storage/sqlite_store.py)
• Semantic rebuild (_build_semantic_baseline) now uses IgnorePatternManager, respecting
  .gitignore and .mcp-index-ignore. Previously indexed test_workspace/ (20,803 Django
  fixture files), causing 7-hour rebuilds. (mcp_server/cli/index_management.py)
• Default ignore patterns expanded: test_workspace/, test_repos/, vendor/,
  third_party/, baml_client/, *_pb2.py, *_pb2_grpc.py.
  (mcp_server/core/ignore_patterns.py)
• code-index-mcp.profiles.yaml base_url now takes precedence over OPENAI_API_BASE
  env default (was reversed, routing oss_high embeddings to wrong endpoint).
  (mcp_server/config/settings.py)
• Corrected oss_high vLLM base_url from 127.0.0.1:8001 to ai:8001.
  (code-index-mcp.profiles.yaml)
• Resolved merge conflicts in treesitter_wrapper.py
• Fixed Python plugin implementation issues
• Tree-sitter byte-offset/char-offset mismatch in Python plugin: symbol names were corrupted in files
  containing multi-byte characters (e.g. em-dashes in docstrings) before the first class/function
  definition. Fixed by using node.text.decode("utf-8") in plugin.py and plugin_semantic.py.
• BM25/FTS path was bypassed when semantic=True but no Qdrant indexer was initialized. Fixed in
  dispatcher_enhanced.py so the FTS path runs whenever the semantic indexer is absent.
• Python plugin _preindex() now excludes htmlcov, .venv, venv, node_modules, __pycache__,
  .git, dist, build directories to prevent junk results from polluting in-memory indexes.

Security

• Added input validation for file paths
• Implemented basic security checks in API endpoints
• Added secret detection patterns

[0.1.0] - TBD

Planned Features

• Complete implementation of C, C++, JavaScript, Dart, and HTML/CSS plugins
• SQLite-based local storage with FTS5
• Full file system watcher implementation
• Performance optimizations and caching
• Authentication and authorization system
• Comprehensive test suite
• Production deployment guide

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Version History

Pre-release Development

• Project inception and architecture design
• Core infrastructure setup
• Initial plugin system implementation