docs: post-cutover + Kuzu 0.11 sweep (#160)

Stale doc references after Phase 6 (Java deletion, #132) and the Kuzu
0.7.1 → 0.11.3 bump (#155 + #159).

- CLAUDE.md / PROJECT_SUMMARY.md: bump Kuzu 0.7.1 → 0.11.3,
  go-sqlite3 1.14.22 → 1.14.44, cobra to 1.10.2; note native FTS.
- AGENTS.md: rewrite "What this repo is" (no more "REST API");
  flip `mvn -B -ntp clean verify` → `go test ./...`; clarify that
  REST + React SPA were deleted in Phase 6 and won't return.
- SECURITY.md: rewrite scope. Drop the dead JAR / serve / REST API /
  React UI / H2 / Neo4j Embedded references. New in-scope list covers
  every codeiq subcommand, the 10 MCP tools (with `run_cypher` mutation
  gate called out), `.codeiq/cache/` (SQLite) + `.codeiq/graph/`
  (Kuzu), and `read_file` path sandboxing. Add the security CI
  workflows (CodeQL, Semgrep, OSV-Scanner, Trivy, Gitleaks, SBOM,
  Socket Security) + perf-gate to the hardening references.
- CHANGELOG.md: populate [Unreleased] with the OOM-fix saga
  (PRs #145-#148), the five correctness fixes (#149-#153), the
  Kuzu 0.7.1 → 0.11.3 bump (#155-#158), the FTS migration (#159),
  the Dependabot config rewrite (#154), and the enrich CLI knobs.

No code changes.

Co-authored-by: Claude Opus 4.7 <noreply@anthropic.com>

Author: aksOps

AGENTS.md

@@ -4,7 +4,7 @@
 
 ## What this repo is
 
-codeiq is a CLI + read-only server that builds a deterministic code-knowledge graph over a codebase. No AI, no external APIs — pure static analysis. See [`/CLAUDE.md`](CLAUDE.md) for the architecture, package map, pipeline, conventions, and gotchas.
+codeiq is a CLI + read-only stdio MCP server that builds a deterministic code-knowledge graph over a codebase. No AI in the index/enrich pipeline; LLM use is opt-in via `codeiq review`. Single static Go binary (CGO for Kuzu + SQLite). See [`/CLAUDE.md`](CLAUDE.md) for the architecture, package map, pipeline, conventions, and gotchas.
 
 ## Pointers, in priority order
 
@@ -22,9 +22,9 @@ codeiq is a CLI + read-only server that builds a deterministic code-knowledge gr
 - **Sign every commit.** The repo-local config (`scripts/setup-git-signed.sh`) makes this automatic; do not rewrite it.
 - **One logical change per commit.** Conventional-commit subjects (`feat:`, `fix:`, `chore:`, `refactor:`, `test:`, `docs:`, `perf:`).
 - **Squash-merge only.** Branch protection rejects merge commits and force-pushes to `main`.
-- **Tests + jacoco gate must pass.** `mvn -B -ntp clean verify` is the contract.
+- **Tests + race + vet must pass.** `cd go && CGO_ENABLED=1 go test ./... -count=1` is the contract; release CI runs `-race` too. 880+ tests today.
 - **Determinism is non-negotiable.** Same input → same output, byte-for-byte. Any new detector ships with a determinism test.
-- **Read-only serving layer.** MCP and REST API on the `serve` path do not mutate. If you find yourself adding `POST /api/<verb>` that writes, stop and reconsider.
+- **Read-only MCP server.** Tool calls never write to the graph. Index/enrich happen only via the CLI commands `codeiq index` / `codeiq enrich`. The Java reference's REST API + React SPA were deleted in Phase 6 cutover (#132) and will not be reintroduced.
 - **No secrets in code.** Repo-level GitHub Actions secrets only.
 
 ## Paperclip / RAN-* coordination

CHANGELOG.md

@@ -14,6 +14,56 @@ for that specific tag for the per-commit details.
 
 ## [Unreleased]
 
+### Fixed
+
+- `codeiq enrich` survives polyglot codebases at `~/projects/` scale (49k
+  files, 15 GiB host). Pre-fix runs OOM-killed at exit 137; now exits 0
+  with peak RSS 1.8–2.2 GiB. PRs #145, #146, #147, #148.
+- Five enrich pipeline correctness fixes that surfaced at scale (each one
+  blocked the next — landed in order):
+  - PR #149: MCP dispatch arg names in `tools_consolidated` (7 modes were
+    permanently returning `INVALID_INPUT`).
+  - PR #150: pipe-delimited Kuzu COPY staging — JSON property values
+    containing commas (e.g. Python `imports`) no longer break the parser.
+  - PR #151: path-qualified SERVICE node IDs — two modules sharing a name
+    in different folders no longer collide on primary key.
+  - PR #152: TOML detector unquotes quoted keys (e.g. airflow's
+    `.cherry_picker.toml` `"check_sha" = ...`).
+  - PR #153: explicit `QUOTE='"', ESCAPE='"'` on Kuzu COPY so RFC-4180
+    quoting round-trips correctly (Istio EDS cluster names with `|`).
+
+### Changed
+
+- **Kuzu 0.7.1 → 0.11.3** (PR #155). Migrates the embedded graph DB to a
+  release with bundled FTS extension and bound `LIMIT`/`SKIP` parameters.
+- **Real FTS replaces CONTAINS predicates** (PR #159). `SearchByLabel`
+  and `SearchLexical` now route through `CALL QUERY_FTS_INDEX` with BM25
+  ranking; CONTAINS fallback retained for pre-enrich graphs. Auto-suffix
+  `*` on single-token queries preserves prefix-match UX. Two indexes
+  created at enrich time:
+  - `code_node_label_fts`   over `(label, fqn_lower)`
+  - `code_node_lexical_fts` over `(prop_lex_comment, prop_lex_config_keys)`
+- **Parameterized `LIMIT`/`SKIP`** across the query layer (PR #159).
+  `intLiteral` helper removed; `fmt.Sprintf("LIMIT %d", n)` replaced with
+  `LIMIT $lim` bindings.
+- **Dropped `stringsToAny` widener** (PR #159). Kuzu 0.11's Go binding
+  accepts `[]string` directly for `IN $param` clauses.
+- **Mutation gate** allow-lists read-only `CALL QUERY_FTS_INDEX` (PR #159);
+  `CREATE_FTS_INDEX` / `DROP_FTS_INDEX` stay blocked under
+  `OpenReadOnly`.
+- **Dependabot config** rewritten (PR #154) — drops the dead Java `maven`
+  (`/`) and `npm` (`/src/main/frontend`) ecosystems, adds `gomod` (`/go`)
+  with groups for `kuzu`, `tree-sitter`, `mcp`, `cobra-viper`, `sqlite`,
+  `test-libs`. Routine bumps land via PRs #155, #156, #157, #158.
+
+### Added
+
+- `codeiq enrich` knobs (PR #147): `--memprofile=<path>` writes a Go
+  heap profile; `--max-buffer-pool=N` overrides the 2 GiB Kuzu cap;
+  `--copy-threads=N` overrides `MaxNumThreads` default.
+- Perf-gate CI step (PR #148): `/usr/bin/time -v codeiq enrich` runs on
+  fixture-multi-lang; fails the build if peak RSS exceeds 300 MB.
+
 ## [v0.3.0] - 2026-05-13
 
 ### Changed

CLAUDE.md

@@ -26,15 +26,16 @@ landing) and `c630245` (release infra).
 
 - **Go 1.25.10** — toolchain pin; module min is 1.25.0 (clamped by the
   MCP SDK's own `go` directive).
-- **Kuzu 0.7.1** (`github.com/kuzudb/go-kuzu`) — embedded graph DB.
-  CGO. v0.11.3 capability matrix documented in `## Gotchas` below.
-- **`mattn/go-sqlite3` 1.14.22** — SQLite analysis cache. CGO.
+- **Kuzu 0.11.3** (`github.com/kuzudb/go-kuzu`) — embedded graph DB.
+  CGO. Native FTS via `CALL CREATE_FTS_INDEX` / `QUERY_FTS_INDEX`.
+  Capability matrix documented in `## Gotchas` below.
+- **`mattn/go-sqlite3` 1.14.44** — SQLite analysis cache. CGO.
 - **`smacker/go-tree-sitter`** — AST parsing for Java / Python /
   TypeScript / Go.
 - **`modelcontextprotocol/go-sdk` v1.6** — stdio MCP server. v1.6 API
   shape: `Server.Serve(ctx, mcpsdk.Transport)`; no `NewStdioTransport`
   helper.
-- **`spf13/cobra`** — CLI framework. Subcommand registration via
+- **`spf13/cobra` 1.10.2** — CLI framework. Subcommand registration via
   `internal/cli` blank imports.
 
 ## Architecture

PROJECT_SUMMARY.md

@@ -22,11 +22,12 @@
 
 - **Go 1.25.10** — toolchain pin in `go/go.mod` (module min 1.25.0,
   clamped by `modelcontextprotocol/go-sdk`).
-- **Kuzu 0.7.1** (`github.com/kuzudb/go-kuzu`) — embedded graph DB.
-- **`mattn/go-sqlite3` 1.14.22** — SQLite analysis cache.
+- **Kuzu 0.11.3** (`github.com/kuzudb/go-kuzu`) — embedded graph DB.
+  Native FTS via `QUERY_FTS_INDEX` (bundled).
+- **`mattn/go-sqlite3` 1.14.44** — SQLite analysis cache.
 - **`smacker/go-tree-sitter`** — AST parsing (Java / Python / TS / Go).
 - **`modelcontextprotocol/go-sdk` v1.6** — stdio MCP server.
-- **`spf13/cobra`** — CLI framework.
+- **`spf13/cobra` 1.10.2** — CLI framework.
 - Manifest files read: `go/go.mod`, `go/go.sum`.
 
 ## Entry points

SECURITY.md

@@ -2,14 +2,14 @@
 
 ## Supported versions
 
-Security fixes are issued against the latest minor release line on Maven Central. While codeiq is pre-1.0 (`0.x.y`) only the **latest** released `0.MINOR.x` line receives backports; older minor lines are EOL the moment a new minor ships.
+Security fixes are issued against the latest minor release line. While codeiq is pre-1.0 (`0.x.y`) only the **latest** released `0.MINOR.x` line receives backports; older minor lines are EOL the moment a new minor ships.
 
 | Version line | Status |
 |---|---|
-| `0.1.x` | Supported (current) |
-| `< 0.1.0` | Unsupported |
+| `0.3.x` | Supported (current — Go single binary) |
+| `0.2.x` and below | Unsupported (Java/Spring Boot reference, deleted at Phase 6 cutover) |
 
-`-SNAPSHOT` builds are development snapshots; they do not receive security fixes by themselves — you should be tracking the latest tagged release.
+Development builds (untagged `main`) are not covered — track the latest tagged release.
 
 ## Reporting a vulnerability
 
@@ -22,8 +22,8 @@ Use one of:
 
 Please include:
 
-- The codeiq version (`java -jar code-iq-*-cli.jar version` or `pom.xml` coordinate).
-- The shortest reproducer you can produce — a CLI command or test case is ideal.
+- The codeiq version (`codeiq --version`).
+- The shortest reproducer you can produce — a CLI command, a test case, or an indexed-fixture path.
 - Your assessment of impact (e.g., RCE, path traversal, info-disclosure, DoS).
 - Whether the issue is in a transitive dependency (please name the dependency + advisory ID if known).
 
@@ -40,26 +40,28 @@ We do not currently run a paid bug bounty.
 
 In-scope:
 
-- The codeiq CLI (`code-iq-*-cli.jar`).
-- The library JAR (`io.github.randomcodespace.iq:code-iq`).
-- The bundled REST API + MCP server (`serve` subcommand) — including path traversal, authn/authz, deserialisation, request smuggling, and SSRF.
-- The bundled React UI assets shipped inside the JAR.
-- The pipeline cache (H2) and graph store (Neo4j Embedded) — including local privilege escalation and data tampering.
+- The `codeiq` CLI binary and every subcommand (`index`, `enrich`, `mcp`, `query`, `find`, `cypher`, `stats`, `flow`, `graph`, `topology`, `review`, `cache`, `plugins`, `config`).
+- The stdio MCP server (`codeiq mcp`) — including its 10 user-facing tools (`graph_summary`, `find_in_graph`, `inspect_node`, `trace_relationships`, `analyze_impact`, `topology_view`, `run_cypher`, `read_file`, `generate_flow`, `review_changes`). The mutation gate on `run_cypher` is in-scope — bypassing it to mutate the read-only Kuzu store is a vulnerability.
+- The pipeline cache (SQLite, `.codeiq/cache/codeiq.sqlite`) and graph store (Kuzu embedded, `.codeiq/graph/codeiq.kuzu`) — including local privilege escalation and data tampering of the indexed graph.
+- File-read sandboxing in `read_file` and `codeiq review` — path traversal out of the indexed root is in-scope.
+- The release pipeline — Goreleaser config, signing keys (cosign keyless via OIDC), GitHub Actions workflows under `.github/workflows/`, and the published artifacts (binary tarballs + checksums + cosign bundles).
 
 Out of scope:
 
 - Vulnerabilities that require pre-existing local code execution on the developer's machine (we ship as a developer tool — by definition you trust the code you point it at).
-- Public-internet attack surface — codeiq does not expose any service to the public internet by default; deploying the `serve` endpoint behind hostile reverse-proxies is out of scope.
-- Findings in third-party services we do not control (Maven Central, GitHub itself, SonarCloud, etc.) — please report those upstream.
+- Public-internet attack surface — codeiq does not expose any service to the public internet. It is a CLI + stdio MCP server only; there is no REST API and no web UI (the Java reference had both; they were deleted in Phase 6 cutover and will not be reintroduced).
+- Vulnerabilities in the LLM endpoint used by `codeiq review` (Ollama local or cloud) — those are the LLM vendor's surface area.
+- Findings in third-party services we do not control (GitHub itself, OpenSSF, Socket Security, etc.) — please report those upstream.
 
 ## Hardening references
 
 - [`shared/runbooks/engineering-standards.md`](shared/runbooks/engineering-standards.md) — CVE policy and quality gates.
 - [`shared/runbooks/rollback.md`](shared/runbooks/rollback.md) §6 — secret rotation flow.
 - `.github/workflows/scorecard.yml` — OpenSSF Scorecard supply-chain checks.
-- GitHub repo-level **CodeQL default setup** (java-kotlin + javascript-typescript + actions) — code scanning, SARIF in the Security tab. Configured under repo Settings → Code security → Code scanning, not via a workflow file (a workflow-driven `codeql.yml` was tried and removed because GitHub rejects duplicate SARIF uploads when default setup is on for the same language).
-- `.github/dependabot.yml` — automated dependency / GHA / npm bumps.
+- `.github/workflows/security.yml` — CodeQL, Semgrep, OSV-Scanner, Trivy, Gitleaks, SBOM, Socket Security on every PR.
+- `.github/workflows/perf-gate.yml` — enrich memory regression gate (300 MB ceiling on fixture-multi-lang).
+- `.github/dependabot.yml` — automated `gomod` + `github-actions` bumps, grouped per ecosystem.
 
 ## Changelog
 
-This file is versioned as part of the repo. Material changes (e.g., raising the supported-versions table, changing the disclosure timeline) are announced via a Release note and a Paperclip board comment.
+This file is versioned as part of the repo. Material changes (e.g., raising the supported-versions table, changing the disclosure timeline) are announced via a Release note.