gitnexus 1.6.10-rc.1 → 1.6.10-rc.100

package/README.md

@@ -43,13 +43,13 @@ To configure MCP for your editor, run `npx gitnexus setup` once — or set it up
 | **Claude Code**          | Yes | Yes    | Yes (PreToolUse + PostToolUse)                                                             | **Full**     |
 | **Cursor**               | Yes | Yes    | Yes (postToolUse, [manual install](../gitnexus-cursor-integration/README.md#hook-install)) | **Full**     |
 | **Antigravity** (Google) | Yes | Yes    | Yes (AfterTool, [Gemini CLI hooks schema](https://geminicli.com/docs/hooks/reference/))    | **Full**     |
-| **Codex**                | Yes | Yes    | —                                                                                          | MCP + Skills |
+| **Codex**                | Yes | Yes    | Yes (PreToolUse + PostToolUse, [Codex hooks](https://developers.openai.com/codex/hooks))   | **Full**     |
 | **OpenCode**             | Yes | Yes    | —                                                                                          | MCP + Skills |
 | **CodeBuddy** (Tencent)  | Yes | Yes    | —                                                                                          | MCP + Skills |
 | **Qoder** (Alibaba)      | Yes | Yes    | —                                                                                          | MCP + Skills |
 | **Windsurf**             | Yes | —      | —                                                                                          | MCP          |
 
-> **Claude Code** gets the deepest integration: MCP tools + agent skills + PreToolUse hooks that automatically enrich grep/glob/bash calls with knowledge graph context + PostToolUse hooks that detect a stale index after commits and prompt the agent to reindex.
+> **Claude Code** and **Codex** get the deepest integration: MCP tools + agent skills + PreToolUse hooks that automatically enrich grep/glob/bash calls with knowledge graph context + PostToolUse hooks that detect a stale index after commits and prompt the agent to reindex.
 
 ### Community Integrations
 
@@ -71,12 +71,23 @@ claude mcp add gitnexus -- npx -y gitnexus@latest mcp
 claude mcp add gitnexus -- cmd /c npx -y gitnexus@latest mcp
 ```
 
-### Codex (full support — MCP + skills)
+### Codex (full support — MCP + skills + hooks)
 
 ```bash
 codex mcp add gitnexus -- npx -y gitnexus@latest mcp
 ```
 
+Codex hooks (PreToolUse graph enrichment + PostToolUse stale-index detection in `~/.codex/hooks.json`, [same schema as Claude Code](https://developers.openai.com/codex/hooks)) need the bundled adapter script, so they are installed by `gitnexus setup -c codex` rather than manually.
+
+Alternatively, install everything as a [Codex plugin](https://developers.openai.com/codex/plugins/build) (MCP + skills + hooks in one step):
+
+```bash
+codex plugin marketplace add abhigyanpatwari/GitNexus
+# then inside Codex: /plugins → install "GitNexus"
+```
+
+> **Codex notes:** SessionStart is intentionally not registered — Codex reads [AGENTS.md natively](https://developers.openai.com/codex/guides/agents-md), which already carries the GitNexus context block. Newly installed hooks need a one-time approval in Codex via `/hooks` before they run. Pick **one** install route (`gitnexus setup -c codex` **or** the plugin): plugin hooks load alongside `~/.codex/hooks.json`, so installing both can fire duplicate hooks per tool call.
+
 ### Cursor / Windsurf
 
 Add to `~/.cursor/mcp.json` (global — works for all projects):
@@ -152,6 +163,16 @@ GitNexus builds a complete knowledge graph of your codebase through a multi-phas
 
 The result is a **LadybugDB graph database** stored locally in `.gitnexus/` with full-text search and semantic embeddings.
 
+### Experimental community detection engine
+
+Community detection uses the bundled Graphology Leiden implementation by default. To test the #2337 Icebug migration path without changing default analyze behavior, set:
+
+```bash
+GITNEXUS_COMMUNITY_ENGINE=icebug npx gitnexus analyze
+```
+
+Supported values are `graphology`, `icebug`, and `auto`. The Icebug path is an experimental probe: GitNexus does not bundle an Icebug native package yet, and if a separately resolvable module is unavailable or its API does not match the expected `Graph.fromCSR` / `ParallelLeidenView` shape, analyze falls back to Graphology and reports the fallback in progress output. Today `auto` is behaviorally identical to `icebug`: both try Icebug and fall back to Graphology, while `graphology` skips the Icebug probe entirely.
+
 ## MCP Tools
 
 Your AI agent gets **17 tools** (15 per-repo + 2 group) automatically:
@@ -209,9 +230,10 @@ gitnexus analyze [path]          # Index a repository (or update stale index)
 gitnexus analyze --repair-fts    # Fast path: rebuild/verify only FTS indexes on existing index data
 gitnexus analyze --force         # Full rebuild: re-parse + graph rebuild + FTS rebuild
 gitnexus analyze --embeddings    # Enable embedding generation (slower, better search)
+gitnexus embeddings install      # Fetch the optional local embedding stack on demand (--cuda, --force)
 gitnexus analyze --skills        # Generate repo-specific skill files from detected communities
 gitnexus analyze --skip-agents-md  # Preserve custom AGENTS.md/CLAUDE.md gitnexus section edits
-gitnexus analyze --skip-skills   # Skip installing .claude/skills/gitnexus/ skill files
+gitnexus analyze --skip-skills   # Skip installing standard .claude/skills/gitnexus-* skill files
 gitnexus analyze --skip-git      # Index folders that are not Git repositories
 gitnexus analyze --workers <n>   # Parse worker pool size (>=1; default: cores-1, capped at 16)
 gitnexus analyze --verbose       # Log skipped files when parsers are unavailable
@@ -227,6 +249,8 @@ gitnexus clean                   # Delete index for current repo
 gitnexus clean --all --force     # Delete all indexes
 gitnexus wiki [path]             # Generate LLM-powered docs from knowledge graph
 gitnexus wiki --model <model>    # Wiki with custom LLM model (default: minimax/minimax-m2.5)
+gitnexus wiki --base-url http://llama-box.local:8080/v1 --allow-insecure-connection llama-box.local
+                                  # Allow an exact LAN/self-hosted HTTP LLM host; env: GITNEXUS_ALLOW_INSECURE_CONNECTION
 gitnexus doctor                  # Show runtime platform capabilities and embedding configuration
 
 # Direct graph queries — the same tools the MCP server exposes, no MCP daemon needed
@@ -260,11 +284,24 @@ Set these env vars to use a remote OpenAI-compatible `/v1/embeddings` endpoint i
 export GITNEXUS_EMBEDDING_URL=http://your-server:8080/v1
 export GITNEXUS_EMBEDDING_MODEL=BAAI/bge-large-en-v1.5
 export GITNEXUS_EMBEDDING_DIMS=1024          # optional, default 384
+export GITNEXUS_EMBEDDING_REQUEST_DIMS=omit  # optional: omit "dimensions", or an integer to override it
 export GITNEXUS_EMBEDDING_API_KEY=your-key   # optional, default: "unused"
+export GITNEXUS_EMBEDDING_MAX_ATTEMPTS=3     # optional, total attempts (1-20)
+export GITNEXUS_EMBEDDING_RETRY_CAP_MS=5000  # optional, maximum retry delay
+export GITNEXUS_EMBEDDING_MIN_INTERVAL_MS=0  # optional, minimum request spacing
 gitnexus analyze . --embeddings
 ```
 
-Works with Infinity, vLLM, TEI, llama.cpp, Ollama, LM Studio, or OpenAI. When unset, local embeddings are used unchanged.
+`GITNEXUS_EMBEDDING_REQUEST_DIMS` controls only the `dimensions` field sent in
+the request body, independently of `GITNEXUS_EMBEDDING_DIMS` (which still
+validates the returned vector's length):
+
+- `omit` (or `none`, `off`, `false`, `0`) — do not send `dimensions` at all, for
+  strict backends that return the right vector size but reject the field.
+- a positive integer — send that value instead of `GITNEXUS_EMBEDDING_DIMS`.
+- unset — send `GITNEXUS_EMBEDDING_DIMS` (the previous behavior).
+
+Works with Infinity, vLLM, TEI, llama.cpp, Ollama, LM Studio, or OpenAI. Retry and pacing settings are provider-neutral; provider-specific limits should be supplied through configuration. When unset, local embeddings are used unchanged.
 
 ## Multi-Repo Support
 
@@ -305,8 +342,11 @@ GitNexus ships with skill files that teach AI agents how to use the tools effect
 - **Refactoring** — Plan safe refactors using dependency mapping
 - **Guide** — GitNexus tool/resource/schema reference for the agent
 - **CLI** — Run analyze/status/clean/wiki commands on request
+- **PDG Query** — Statement-level control/data dependence queries (`--pdg` index)
+- **Taint Analysis** — Source→sink data-flow findings (`--pdg` index)
+- **Plan / Work / Review / LFG** — The engineering family: implementation-ready plans, gated plan execution, graph-backed change review with taint + expert lenses, and the end-to-end pipeline
 
-Installed automatically by both `gitnexus analyze` (per-repo) and `gitnexus setup` (global). Run `gitnexus analyze --skills` to additionally generate repo-specific skills for each detected functional area under `.claude/skills/generated/`.
+Installed automatically by both `gitnexus analyze` (per-repo) and `gitnexus setup` (global). Run `gitnexus analyze --skills` to additionally generate each detected functional area as a direct project skill under `.claude/skills/gitnexus-area-<name>/`.
 
 ## Requirements
 
@@ -409,19 +449,43 @@ If `npm install -g gitnexus` fails on native modules:
 npm install -g gitnexus
 ```
 
+### Installation fails behind an HTTP proxy (`onnxruntime-node` postinstall)
+
+`onnxruntime-node`'s postinstall downloads optional CUDA GPU binaries from `api.nuget.org` — outside the npm registry, so registry mirrors don't cover it, and its proxy layer (`global-agent`) ignores the standard `HTTP_PROXY`/`HTTPS_PROXY` variables and rejects 302 redirects ([#2370](https://github.com/abhigyanpatwari/GitNexus/issues/2370)).
+
+Since the packages are optional dependencies, a failed download no longer breaks `npm install -g gitnexus` — npm skips the embedding stack and everything else works. The stack then **self-heals on demand**: the first `gitnexus analyze --embeddings` (or an explicit `gitnexus embeddings install`) fetches it through your configured npm registry — mirrors and proxies apply, no NuGet download involved — into `~/.gitnexus/embedding-runtime`.
+
+```bash
+# heal a proxy-degraded install manually (CPU embeddings; registry-only)
+gitnexus embeddings install
+
+# reinstall into the prefix even when the stack already resolves
+gitnexus embeddings install --force
+
+# CUDA GPU hosts: also fetch GPU binaries (NuGet; set the proxy global-agent reads)
+GLOBAL_AGENT_HTTPS_PROXY=<proxy-url> gitnexus embeddings install --cuda
+```
+
+The prefix defaults to `~/.gitnexus/embedding-runtime`; set `GITNEXUS_EMBEDDING_RUNTIME_DIR` to install it elsewhere (e.g. a writable path in a container).
+
+> **Node requirement for the on-demand prefix:** the self-heal loads the prefixed packages via `module.registerHooks`, available on Node **≥ 22.15** (on the 22.x line) or **≥ 23.5** (on the 23.x line). On an older Node the packages install but can't be loaded from the prefix — reinstall them into the install itself instead (works on every supported Node): `ONNXRUNTIME_NODE_INSTALL=skip npm install -g gitnexus` (Windows: `set ONNXRUNTIME_NODE_INSTALL=skip && npm install -g gitnexus`). Skipping only the CUDA download keeps full CPU embeddings (CPU embeddings don't need it). Check the result any time with `gitnexus doctor` (Embeddings → Support line).
+
 ### Analyze warns about unavailable FTS or VECTOR extensions
 
-GitNexus uses optional DuckDB extensions for BM25 and vector search. The `gitnexus serve` and MCP read paths only ever try to `LOAD` the extensions — they never block on a network install. The `analyze` command, by default, attempts one bounded out-of-process `INSTALL` if `LOAD` fails and proceeds even when that install times out, so the index is always written to disk; BM25/vector search degrade gracefully until the extensions become available.
+GitNexus uses optional DuckDB extensions for BM25 and vector search. The `gitnexus serve` and MCP read paths only ever try to `LOAD` the extensions — they never block on a network install. The `analyze` command, by default, attempts one bounded out-of-process install if `LOAD` fails (a plain `INSTALL` to download a missing extension, escalating to `FORCE INSTALL` only when the `LOAD` error shows the existing file is broken or truncated, so a permanent non-file failure does not re-download on every run) and proceeds even when that install times out, so the index is always written to disk; BM25/vector search degrade gracefully until the extensions become available.
 
 Configure the behavior with these environment variables:
 
-| Variable                                     | Values                       | Default             | Effect                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  |
-| -------------------------------------------- | ---------------------------- | ------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| `GITNEXUS_LBUG_EXTENSION_INSTALL`            | `auto`, `load-only`, `never` | `auto`              | `auto` runs one bounded INSTALL if LOAD fails. `load-only` only uses already-installed extensions (recommended for offline / firewalled environments). `never` skips optional extensions entirely.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |
-| `GITNEXUS_LBUG_EXTENSION_INSTALL_TIMEOUT_MS` | positive integer             | `15000`             | Wall-clock budget for the out-of-process `INSTALL` child before it is killed.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           |
-| `GITNEXUS_FTS_STEMMER`                       | supported LadybugDB stemmer  | `porter`            | Stemmer used when rebuilding BM25/FTS indexes. Use `none` for CJK-heavy repositories, or a language stemmer such as `german`, `french`, or `spanish` when that better matches repository comments and identifiers. Re-run `gitnexus analyze --repair-fts` after changing it.                                                                                                                                                                                                                                                                                                                                                                                                                            |
-| `GITNEXUS_FTS_CJK_SEGMENTATION`              | `none`, `bigram`             | `none`              | `bigram` inserts overlapping character-bigram boundaries into Chinese/Japanese Han-ideograph spans in `content`/`description` before FTS indexing, so LadybugDB's space-only tokenizer can see sub-phrase word boundaries. Scoped to CJK Unified Ideographs only — Japanese Hiragana/Katakana and Korean Hangul are not currently segmented. Unlike `GITNEXUS_FTS_STEMMER`, this rewrites stored text — enabling it on an already-indexed repo requires a full `gitnexus analyze --force`; neither `--repair-fts` nor a plain incremental `analyze` applies it to previously-indexed files. Set the same value wherever `analyze` and search-serving processes (CLI query, MCP server, web server) run. |
-| `GITNEXUS_WAL_CHECKPOINT_THRESHOLD`          | integer `>= -1`              | `67108864` (64 MiB) | LadybugDB WAL auto-checkpoint threshold during analyze (bytes). Auto-checkpoint remains enabled; `-1` keeps Ladybug's stock ~16 MiB. Larger thresholds reduce checkpoint frequency but increase the WAL size at rotation time — choose a smaller value on disk-constrained environments.                                                                                                                                                                                                                                                                                                                                                                                                                |
+| Variable                                     | Values                         | Default             | Effect                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  |
+| -------------------------------------------- | ------------------------------ | ------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| `GITNEXUS_LBUG_EXTENSION_INSTALL`            | `auto`, `load-only`, `never`   | `auto`              | `auto` runs one bounded install if LOAD fails — a plain `INSTALL`, escalating to `FORCE INSTALL` only when the LOAD error shows the present extension file is broken. `load-only` only uses already-installed extensions (recommended for offline / firewalled environments). `never` skips optional extensions entirely.                                                                                                                                                                                                                                                                                                                                                                               |
+| `GITNEXUS_LBUG_EXTENSION_INSTALL_TIMEOUT_MS` | positive integer               | `15000`             | Wall-clock budget for the out-of-process extension-install child before it is killed.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   |
+| `GITNEXUS_FTS_STEMMER`                       | supported LadybugDB stemmer    | `porter`            | Stemmer used when rebuilding BM25/FTS indexes. Use `none` for CJK-heavy repositories, or a language stemmer such as `german`, `french`, or `spanish` when that better matches repository comments and identifiers. Re-run `gitnexus analyze --repair-fts` after changing it.                                                                                                                                                                                                                                                                                                                                                                                                                            |
+| `GITNEXUS_FTS_CJK_SEGMENTATION`              | `none`, `bigram`               | `none`              | `bigram` inserts overlapping character-bigram boundaries into Chinese/Japanese Han-ideograph spans in `content`/`description` before FTS indexing, so LadybugDB's space-only tokenizer can see sub-phrase word boundaries. Scoped to CJK Unified Ideographs only — Japanese Hiragana/Katakana and Korean Hangul are not currently segmented. Unlike `GITNEXUS_FTS_STEMMER`, this rewrites stored text — enabling it on an already-indexed repo requires a full `gitnexus analyze --force`; neither `--repair-fts` nor a plain incremental `analyze` applies it to previously-indexed files. Set the same value wherever `analyze` and search-serving processes (CLI query, MCP server, web server) run. |
+| `GITNEXUS_COMMUNITY_ENGINE`                  | `graphology`, `icebug`, `auto` | `graphology`        | Community-detection engine used during analyze. `graphology` uses the bundled default path. `icebug` and `auto` currently behave identically: both try the experimental Icebug CSR path and fall back to Graphology if the optional native module is unavailable or incompatible.                                                                                                                                                                                                                                                                                                                                                                                                                       |
+| `GITNEXUS_WAL_CHECKPOINT_THRESHOLD`          | integer `>= -1`                | `67108864` (64 MiB) | LadybugDB WAL auto-checkpoint threshold during analyze (bytes). Auto-checkpoint remains enabled; `-1` keeps Ladybug's stock ~16 MiB. Larger thresholds reduce checkpoint frequency but increase the WAL size at rotation time — choose a smaller value on disk-constrained environments.                                                                                                                                                                                                                                                                                                                                                                                                                |
+| `GITNEXUS_LBUG_BUFFER_POOL_SIZE`             | integer `>= 0` (bytes)         | min(2 GiB, 80% RAM) | LadybugDB buffer-pool ceiling for every GitNexus database (analyze, MCP server, serve, group bridges). Bounded so a long-lived `gitnexus mcp` process or a large incremental `analyze` cannot grow toward LadybugDB's native 80%-of-RAM default and OOM the host (#2557). `0` restores that native unbounded default; invalid values warn and fall back to the default. During `analyze` the pool is right-sized to the graph and, on non-4 KiB-page hosts (Apple Silicon 16 KiB, Ascend/aarch64 64 KiB), scaled by the page-size granule ratio up to min(2 GiB × pageSize/4 KiB, 80% RAM) (#2631); this env var overrides all of that as an absolute value.                                                                                                                                                                                                                                                                                                                                  |
+| `GITNEXUS_LBUG_MAX_DB_SIZE`                  | positive integer (bytes)       | `17179869184` (16 GiB) | Upper bound for a single LadybugDB database file. This is an mmap/disk-address-space ceiling, not a memory limit — it does not constrain the buffer pool (use `GITNEXUS_LBUG_BUFFER_POOL_SIZE` for that). Raise it when indexing genuinely huge monorepos; invalid values silently fall back to the default.                                                                                                                                                                                                                                                                                                                                                                                             |
 
 ```bash
 # Offline/airgapped: never reach the network for extensions
@@ -447,9 +511,19 @@ For very large repositories:
 # Increase Node.js heap size
 NODE_OPTIONS="--max-old-space-size=16384" npx gitnexus analyze
 
-# Exclude large directories
+# Exclude large directories (this repo only)
 echo "vendor/" >> .gitnexusignore
 echo "dist/" >> .gitnexusignore
+
+# Exclude a directory across every repo you index, without touching each
+# repo's own .gitnexusignore or needing push/commit access to it. GitNexus
+# reads the same sources `git` itself does: core.excludesFile (all repos)
+# and $GIT_DIR/info/exclude (this repo only, untracked). A repo's own
+# .gitignore/.gitnexusignore can still override either with a `!pattern`
+# negation. Skip both entirely with GITNEXUS_NO_GLOBAL_IGNORE=1.
+git config --global core.excludesFile ~/.gitignore_global   # applies to every repo
+echo "docs/" >> ~/.gitignore_global
+echo "build/" >> .git/info/exclude                          # this repo only, untracked
 ```
 
 ### Large files are being skipped
@@ -484,13 +558,16 @@ For repositories with very large source files, `GITNEXUS_WORKER_SUB_BATCH_MAX_BY
 
 ### Worker pool resilience tuning
 
-Three env vars expose the pool's resilience layers (respawn budget, cumulative-timeout cap, circuit breaker). Defaults are tuned for typical repos; bump them when an analyze legitimately needs more retries, or lower them to fail-fast on a known-bad shape.
+Four env vars expose the pool's resilience layers (respawn budget, cumulative-timeout cap, circuit breaker, startup handshake). Defaults are tuned for typical repos; bump them when an analyze legitimately needs more retries, or lower them to fail-fast on a known-bad shape.
 
-| Variable                                        | Default                 | Effect                                                                                                                |
-| ----------------------------------------------- | ----------------------- | --------------------------------------------------------------------------------------------------------------------- |
-| `GITNEXUS_WORKER_MAX_RESPAWNS_PER_SLOT`         | `3`                     | Max replacement spawns per slot before the slot is dropped from the active rotation.                                  |
-| `GITNEXUS_WORKER_MAX_CUMULATIVE_TIMEOUT_MS`     | `5 × subBatchTimeoutMs` | Total retry wall-time budget per job before quarantining. Bounds exponentially-growing retry waits.                   |
-| `GITNEXUS_WORKER_CONSECUTIVE_FAILURE_THRESHOLD` | `max(3, poolSize)`      | Per-slot consecutive deaths before the pool's circuit breaker trips. After tripping, dispatches require a fresh pool. |
+| Variable                                        | Default                 | Effect                                                                                                                                                                                           |
+| ----------------------------------------------- | ----------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
+| `GITNEXUS_WORKER_MAX_RESPAWNS_PER_SLOT`         | `3`                     | Max replacement spawns per slot before the slot is dropped from the active rotation.                                                                                                             |
+| `GITNEXUS_WORKER_MAX_CUMULATIVE_TIMEOUT_MS`     | `5 × subBatchTimeoutMs` | Total retry wall-time budget per job before quarantining. Bounds exponentially-growing retry waits.                                                                                              |
+| `GITNEXUS_WORKER_CONSECUTIVE_FAILURE_THRESHOLD` | `max(3, poolSize)`      | Per-slot consecutive deaths before the pool's circuit breaker trips. After tripping, dispatches require a fresh pool.                                                                            |
+| `GITNEXUS_WORKER_SHUTDOWN_DRAIN_MS`             | `30000`                 | Max wait at pool shutdown for a retired worker still inside native code — terminated at its next JS-safe point instead of mid-native-call, which would abort the process (`Napi::Error`, #2432). |
+| `GITNEXUS_WORKER_READY_TIMEOUT_MS`              | `5000`                  | Startup budget for a parse worker to load its grammar bindings and report `{type:'ready'}`. Slots that miss it are treated as startup crashes. Raise it on a slow or heavily loaded host where a full pool cold-starting concurrently needs more than 5s. |
+| `GITNEXUS_CPP_CAPTURE_BUDGET_MS`                | `20000`                 | Per-file wall-clock budget for C++ capture extraction; on breach the file keeps partial captures with a warning (#2432). `0` expires immediately.                                                |
 
 ### Graph cleanup tuning
 
@@ -502,17 +579,26 @@ After scope resolution, analyze prunes inert block-local value symbols (a functi
 
 Programmatic callers can pass `keepLocalValueSymbols: true` in `PipelineOptions` instead of setting the env var.
 
-### Hook augmentation/notifications are silently skipped
+### Hook augmentation and skip diagnostics
 
-The Claude Code / Antigravity hooks intentionally stay **silent** on normal skip
+The Claude Code / Antigravity hooks keep their **stderr** silent on normal skip
 paths so strict hook runners (e.g. Codex `PreToolUse`) never see unexpected
-output. A search may not be augmented — or a stale-index reminder may not appear
-on stderr — when the GitNexus MCP server owns the repo DB, when the DB-lock probe
-times out and fails closed, or when the index is already current.
-
-To see why a hook skipped, set `GITNEXUS_DEBUG=1` and re-run the action — the hook
-writes the reason (e.g. `[GitNexus] augment skipped: MCP server owns DB`) and the
-stale-index hint to its stderr:
+diagnostic output.
+
+When a GitNexus process holds the repo DB write lock (the common case — the MCP
+server is running, or the DB-lock probe timed out and failed closed), the local
+CLI `augment` can't run (LadybugDB is single-writer). Rather than drop the
+augmentation, the hook hands the agent a short, conditional MCP-query hint on
+stdout (the sanctioned `additionalContext` channel) — _"if the GitNexus MCP tools
+are live in this session, call `query` …"_ — so an agent that has the tools can
+still fetch graph-ranked context. The hint is throttled to at most once per repo
+per window (`GITNEXUS_MCP_HINT_THROTTLE_MS`, default 10 min; `0` disables), so an
+owner-locked session isn't nudged on every search. A stale-index reminder, or an
+already-current index, stays silent.
+
+To see why a hook skipped the CLI augment, set `GITNEXUS_DEBUG=1` and re-run the
+action — the hook writes the reason (e.g. `[GitNexus] augment skipped: MCP server
+owns DB`) and the stale-index hint to its stderr:
 
 ```bash
 GITNEXUS_DEBUG=1 <your command>   # surfaces hook skip/diagnostic reasons on stderr

package/dist/_shared/graph/types.d.ts

@@ -55,14 +55,14 @@ export type NodeProperties = {
     [key: string]: unknown;
 };
 export type RelationshipType = 'CONTAINS' | 'CALLS' | 'INHERITS' | 'METHOD_OVERRIDES' | 'METHOD_IMPLEMENTS' | 'IMPORTS' | 'USES' | 'DEFINES' | 'DECORATES' | 'IMPLEMENTS' | 'EXTENDS' | 'HAS_METHOD' | 'HAS_PROPERTY' | 'ACCESSES' | 'MEMBER_OF' | 'STEP_IN_PROCESS' | 'HANDLES_ROUTE' | 'FETCHES' | 'HANDLES_TOOL' | 'ENTRY_POINT_OF' | 'WRAPS' | 'QUERIES'
-/** Dependency-injection edge: a consumer class receives every implementer
- *  of interface `T` via a container-injected collection-typed field
- *  (`List<T>`, `Set<T>`, `Collection<T>`, or `Map<K,T>`). Precondition: the
- *  field carries an injection annotation recognized by a per-language
- *  matcher registered in `di-extractors/` (Java/Spring today: `@Autowired`
- *  or `@Inject`; `@Resource` is excluded — by-name-first semantics).
- *  Source = the consumer Class node (the one owning the field).
- *  Target = an implementing Class node.
+/** Dependency-injection edge: a consumer class receives a likely provider
+ *  through constructor, field, method, or collection injection. A
+ *  per-language resolver identifies the site and provider metadata; the
+ *  shared DI phase uses type heritage, qualifier names, and preferred
+ *  provider markers to resolve it. Ambiguous single injection is represented
+ *  by multiple lower-confidence edges instead of a fabricated exact target.
+ *  Source = the consumer Class node (the one owning the injection site).
+ *  Target = a concrete provider Class node.
  *  Framework specifics live in the `reason` payload (e.g.
  *  `Spring DI: @Autowired List<T>`), not in this type contract.
  *  Lets Cypher queries trace which beans the container injects into a given

package/dist/_shared/index.d.ts

@@ -22,6 +22,7 @@ export { resolveTypeRef } from './scope-resolution/resolve-type-ref.js';
 export type { ResolveTypeRefContext } from './scope-resolution/resolve-type-ref.js';
 export type { ParsedFile } from './scope-resolution/parsed-file.js';
 export type { ReferenceSite, ReferenceKind, CallForm } from './scope-resolution/reference-site.js';
+export type { CallableFlowOperand, CallableFlowExpectedSignature, CallableFlowPassingMode, CallableFlowInvocationKind, CallableFlowSeedSite, CallableFlowCopySite, CallableFlowAliasSite, CallableFlowAddressSite, CallableFlowStoreSite, CallableFlowLoadSite, CallableFlowFormalSite, CallableFlowArgumentSite, CallableFlowInvokeSite, CallableFlowSite, } from './scope-resolution/callable-flow-site.js';
 export { buildMethodDispatchIndex } from './scope-resolution/method-dispatch-index.js';
 export type { MethodDispatchIndex, MethodDispatchInput, } from './scope-resolution/method-dispatch-index.js';
 export { finalize } from './scope-resolution/finalize-algorithm.js';

package/dist/_shared/index.d.ts.map

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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AASA,mBAAmB;AACnB,OAAO,EACL,WAAW,EACX,cAAc,EACd,SAAS,EACT,oBAAoB,GACrB,MAAM,4BAA4B,CAAC;AAGpC,mBAAmB;AACnB,OAAO,EAAE,kBAAkB,EAAE,MAAM,gBAAgB,CAAC;AACpD,OAAO,EACL,uBAAuB,EACvB,6BAA6B,EAC7B,uBAAuB,GACxB,MAAM,yBAAyB,CAAC;AAiCjC,8DAA8D;AAC9D,OAAO,EAAE,eAAe,EAAE,wBAAwB,EAAE,MAAM,wCAAwC,CAAC;AACnG,OAAO,EAAE,eAAe,EAAE,MAAM,uCAAuC,CAAC;AAGxE,yDAAyD;AACzD,OAAO,EACL,uBAAuB,EACvB,oBAAoB,GACrB,MAAM,+CAA+C,CAAC;AAGvD,sEAAsE;AACtE,OAAO,EAAE,aAAa,EAAE,MAAM,iCAAiC,CAAC;AAEhE,OAAO,EAAE,qBAAqB,EAAE,MAAM,0CAA0C,CAAC;AAEjF,OAAO,EAAE,uBAAuB,EAAE,MAAM,4CAA4C,CAAC;AAGrF,gEAAgE;AAChE,yEAAyE;AACzE,2DAA2D;AAC3D,OAAO,EAAE,cAAc,EAAE,MAAM,wCAAwC,CAAC;AAuBxE,oFAAoF;AACpF,OAAO,EAAE,wBAAwB,EAAE,MAAM,6CAA6C,CAAC;AAMvF,uEAAuE;AACvE,OAAO,EAAE,QAAQ,EAAE,MAAM,0CAA0C,CAAC;AAUpE,sEAAsE;AACtE,OAAO,EAAE,kBAAkB,EAAE,MAAM,iDAAiD,CAAC;AAErF,OAAO,EAAE,mBAAmB,EAAE,MAAM,kDAAkD,CAAC;AAKvF,OAAO,EAAE,kBAAkB,EAAE,MAAM,iDAAiD,CAAC;AAKrF,OAAO,EAAE,kBAAkB,EAAE,MAAM,iDAAiD,CAAC;AAErF,OAAO,EAAE,UAAU,EAAE,MAAM,8CAA8C,CAAC;AAE1E,OAAO,EAAE,eAAe,EAAE,MAAM,mDAAmD,CAAC;AAEpF,OAAO,EAAE,eAAe,EAAE,sBAAsB,EAAE,MAAM,2CAA2C,CAAC;AAEpG,OAAO,EACL,gCAAgC,EAChC,kBAAkB,GACnB,MAAM,6CAA6C,CAAC;AAErD,OAAO,EACL,WAAW,EACX,YAAY,EACZ,WAAW,EACX,WAAW,GACZ,MAAM,0CAA0C,CAAC;AAUlD,2EAA2E;AAC3E,OAAO,EAAE,WAAW,EAAE,sBAAsB,EAAE,MAAM,gCAAgC,CAAC;AAErF,OAAO,EACL,cAAc,EACd,cAAc,EACd,uBAAuB,GACxB,MAAM,kCAAkC,CAAC;AAE1C,OAAO,EAAE,kBAAkB,EAAE,MAAM,sCAAsC,CAAC;AAG1E,8EAA8E;AAC9E,wEAAwE;AACxE,wEAAwE;AACxE,8DAA8D;AAC9D,OAAO,EAAE,SAAS,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAC;AAEtE,OAAO,EAAE,cAAc,EAAE,gBAAgB,EAAE,UAAU,EAAE,MAAM,mCAAmC,CAAC;AAEjG,OAAO,EACL,cAAc,EACd,4BAA4B,EAC5B,kBAAkB,EAClB,eAAe,GAChB,MAAM,mCAAmC,CAAC;AAG3C,mDAAmD;AACnD,OAAO,EACL,+BAA+B,EAC/B,6BAA6B,EAC7B,4BAA4B,EAC5B,sBAAsB,EACtB,gBAAgB,EAChB,wBAAwB,EACxB,cAAc,GACf,MAAM,sCAAsC,CAAC"}

package/dist/_shared/integrations/resilient-fetch.d.ts

@@ -25,6 +25,8 @@ export interface ResilientFetchOptions {
     breakerOptions?: CircuitBreakerOptions;
     /** Tuning knobs for the retry helper. */
     retry?: Partial<Pick<RetryOptions, 'maxAttempts' | 'baseDelayMs' | 'capDelayMs'>> & {
+        /** Upper bound on a single Retry-After wait. Defaults to RETRY_AFTER_CAP_MS. */
+        retryAfterCapMs?: number;
         sleep?: RetryOptions['sleep'];
         random?: RetryOptions['random'];
     };
@@ -64,7 +66,7 @@ export declare function classifyOutcome(result: {
 } | {
     kind: 'response';
     resp: Response;
-}, now: () => number): Outcome;
+}, now: () => number, retryAfterCapMs?: number): Outcome;
 /** Final error thrown when retries are exhausted on a 5xx / 429. */
 export declare class ResilientFetchExhaustedError extends Error {
     readonly response: Response;

package/dist/_shared/integrations/resilient-fetch.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"resilient-fetch.d.ts","sourceRoot":"","sources":["../../src/integrations/resilient-fetch.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EACL,cAAc,EACd,gBAAgB,EAEhB,KAAK,qBAAqB,EAC3B,MAAM,sBAAsB,CAAC;AAC9B,OAAO,EAAoB,KAAK,YAAY,EAAE,MAAM,YAAY,CAAC;AAEjE,OAAO,EAAE,gBAAgB,EAAE,CAAC;AAE5B,MAAM,WAAW,qBAAqB;IACpC,8EAA8E;IAC9E,SAAS,CAAC,EAAE,OAAO,KAAK,CAAC;IACzB;;;;OAIG;IACH,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,2EAA2E;IAC3E,OAAO,CAAC,EAAE,cAAc,CAAC;IACzB,kEAAkE;IAClE,cAAc,CAAC,EAAE,qBAAqB,CAAC;IACvC,yCAAyC;IACzC,KAAK,CAAC,EAAE,OAAO,CAAC,IAAI,CAAC,YAAY,EAAE,aAAa,GAAG,aAAa,GAAG,YAAY,CAAC,CAAC,GAAG;QAClF,gFAAgF;QAChF,eAAe,CAAC,EAAE,MAAM,CAAC;QACzB,KAAK,CAAC,EAAE,YAAY,CAAC,OAAO,CAAC,CAAC;QAC9B,MAAM,CAAC,EAAE,YAAY,CAAC,QAAQ,CAAC,CAAC;KACjC,CAAC;IACF,6EAA6E;IAC7E,GAAG,CAAC,EAAE,MAAM,MAAM,CAAC;CACpB;AAED,+EAA+E;AAC/E,eAAO,MAAM,kBAAkB,QAAS,CAAC;AAQzC;;;;GAIG;AACH,wBAAgB,eAAe,CAAC,KAAK,EAAE,MAAM,GAAG,IAAI,EAAE,GAAG,GAAE,MAAM,MAAiB,GAAG,MAAM,GAAG,IAAI,CAejG;AAED,wEAAwE;AACxE,KAAK,OAAO,GACR;IAAE,IAAI,EAAE,SAAS,CAAC;IAAC,IAAI,EAAE,QAAQ,CAAA;CAAE,GACnC;IAAE,IAAI,EAAE,iBAAiB,CAAC;IAAC,IAAI,EAAE,QAAQ,CAAA;CAAE,GAC3C;IAAE,IAAI,EAAE,kBAAkB,CAAC;IAAC,IAAI,EAAE,QAAQ,CAAC;IAAC,OAAO,EAAE,MAAM,GAAG,SAAS,CAAA;CAAE,GACzE;IAAE,IAAI,EAAE,kBAAkB,CAAC;IAAC,GAAG,EAAE,OAAO,CAAA;CAAE,GAC1C;IAAE,IAAI,EAAE,mBAAmB,CAAC;IAAC,GAAG,EAAE,OAAO,CAAA;CAAE,CAAC;AAEhD,+BAA+B;AAC/B,wBAAgB,eAAe,CAC7B,MAAM,EAAE;IAAE,IAAI,EAAE,OAAO,CAAC;IAAC,GAAG,EAAE,OAAO,CAAA;CAAE,GAAG;IAAE,IAAI,EAAE,UAAU,CAAC;IAAC,IAAI,EAAE,QAAQ,CAAA;CAAE,EAC9E,GAAG,EAAE,MAAM,MAAM,EACjB,eAAe,SAAqB,GACnC,OAAO,CAiCT;AAcD,oEAAoE;AACpE,qBAAa,4BAA6B,SAAQ,KAAK;aAEzB,QAAQ,EAAE,QAAQ;IAD9C,SAAkB,IAAI,kCAAkC;gBAC5B,QAAQ,EAAE,QAAQ;CAG/C;AAED;;;;;;;;;;;;;;;;;;;;;;;GAuBG;AACH,wBAAsB,cAAc,CAClC,KAAK,EAAE,MAAM,GAAG,GAAG,EACnB,IAAI,EAAE,WAAW,GAAG,SAAS,EAC7B,IAAI,GAAE,qBAA0B,GAC/B,OAAO,CAAC,QAAQ,CAAC,CA+GnB"}

package/dist/_shared/integrations/resilient-fetch.js

@@ -41,7 +41,7 @@ export function parseRetryAfter(value, now = Date.now) {
     return delta >= 0 ? delta : 0;
 }
 /** Exported for unit tests. */
-export function classifyOutcome(result, now) {
+export function classifyOutcome(result, now, retryAfterCapMs = RETRY_AFTER_CAP_MS) {
     if (result.kind === 'error') {
         // Both timer-fired aborts (`AbortSignal.timeout()` → `TimeoutError`)
         // and caller-driven aborts (`AbortController.abort()` → `AbortError`)
@@ -67,7 +67,7 @@ export function classifyOutcome(result, now) {
         return {
             kind: 'retryable-status',
             resp,
-            afterMs: parsed !== null ? Math.min(parsed, RETRY_AFTER_CAP_MS) : undefined,
+            afterMs: parsed !== null ? Math.min(parsed, retryAfterCapMs) : undefined,
         };
     }
     if (resp.status >= 500)
@@ -125,6 +125,7 @@ export async function resilientFetch(input, init, opts = {}) {
         maxAttempts: opts.retry?.maxAttempts ?? DEFAULT_RETRY.maxAttempts,
         baseDelayMs: opts.retry?.baseDelayMs ?? DEFAULT_RETRY.baseDelayMs,
         capDelayMs: opts.retry?.capDelayMs ?? DEFAULT_RETRY.capDelayMs,
+        retryAfterCapMs: opts.retry?.retryAfterCapMs ?? RETRY_AFTER_CAP_MS,
     };
     const sleep = opts.retry?.sleep ?? defaultSleep;
     const random = opts.retry?.random ?? Math.random;
@@ -149,7 +150,7 @@ export async function resilientFetch(input, init, opts = {}) {
         catch (err) {
             result = { kind: 'error', err };
         }
-        const outcome = classifyOutcome(result, now);
+        const outcome = classifyOutcome(result, now, retryConfig.retryAfterCapMs);
         switch (outcome.kind) {
             case 'success':
                 breaker.recordSuccess();

package/dist/_shared/integrations/resilient-fetch.js.map

@@ -1 +1 @@
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package/dist/_shared/scope-resolution/callable-flow-site.d.ts

@@ -0,0 +1,110 @@
+/**
+ * Always-on callable-value-flow facts produced during scope extraction.
+ *
+ * These records deliberately contain no parser nodes or provider-private
+ * objects: they cross the worker, disk-cache, and ParsedFile-store boundaries.
+ * Language providers recognize syntax and emit `@callable-flow.*` captures;
+ * the central extractor attaches lexical scope ids and materializes this
+ * language-neutral representation.
+ */
+import type { ParameterTypeClass } from './symbol-definition.js';
+import type { Range, ScopeId } from './types.js';
+/** A lexical binding or abstract indirection cell used by a flow fact. */
+export interface CallableFlowOperand {
+    /** Provider-normalized lexical binding name. */
+    readonly name: string;
+    readonly inScope: ScopeId;
+    readonly atRange: Range;
+    /** Number of dereference operators applied at this occurrence. */
+    readonly indirection: number;
+    /** Whether this occurrence explicitly takes the binding's address. */
+    readonly addressOf: boolean;
+    /**
+     * Provider-normalized expression role. `binding` is the conservative
+     * default; the other variants prove the occurrence denotes a callable
+     * designator rather than a value produced by an expression.
+     */
+    readonly expressionKind?: 'binding' | 'callable-designator' | 'bound-member' | 'anonymous-callable';
+    /** Qualified spelling retained for receiver/member-aware lookup. */
+    readonly qualifiedName?: string;
+}
+/** Callable shape used to disambiguate overload sets when syntax supplies it. */
+export interface CallableFlowExpectedSignature {
+    readonly parameterCount?: number;
+    readonly parameterTypes?: readonly string[];
+    readonly parameterTypeClasses?: readonly ParameterTypeClass[];
+    /** C++ member-function cv qualifier when the declarator supplies it. */
+    readonly isConst?: boolean;
+}
+export type CallableFlowPassingMode = 'value' | 'reference' | 'pointer';
+export interface CallableFlowSeedSite {
+    readonly kind: 'seed';
+    readonly destination: CallableFlowOperand;
+    /** Simple callable name used for lexical lookup. */
+    readonly targetName: string;
+    /** Optional provider-normalized qualified spelling (for example `Base.method`). */
+    readonly targetQualifiedName?: string;
+    readonly targetRange: Range;
+    readonly expectedSignature?: CallableFlowExpectedSignature;
+}
+export interface CallableFlowCopySite {
+    readonly kind: 'copy';
+    readonly source: CallableFlowOperand;
+    readonly destination: CallableFlowOperand;
+}
+/** True identity (for example a C++ reference), modelled bidirectionally. */
+export interface CallableFlowAliasSite {
+    readonly kind: 'alias';
+    readonly source: CallableFlowOperand;
+    readonly destination: CallableFlowOperand;
+}
+/** `destination` receives the abstract address of `source`. */
+export interface CallableFlowAddressSite {
+    readonly kind: 'address';
+    readonly source: CallableFlowOperand;
+    readonly destination: CallableFlowOperand;
+}
+/** Targets in `source` flow into every abstract cell reached by `pointer`. */
+export interface CallableFlowStoreSite {
+    readonly kind: 'store';
+    readonly source: CallableFlowOperand;
+    readonly pointer: CallableFlowOperand;
+}
+/** Targets in every abstract cell reached by `pointer` flow into `destination`. */
+export interface CallableFlowLoadSite {
+    readonly kind: 'load';
+    readonly pointer: CallableFlowOperand;
+    readonly destination: CallableFlowOperand;
+}
+/** Maps a callable definition's parameter position to its lexical binding. */
+export interface CallableFlowFormalSite {
+    readonly kind: 'formal';
+    readonly ownerName: string;
+    readonly ownerRange: Range;
+    readonly parameterIndex: number;
+    readonly binding: CallableFlowOperand;
+    readonly passingMode: CallableFlowPassingMode;
+    readonly expectedSignature?: CallableFlowExpectedSignature;
+}
+/** Maps one real call-site argument position to its source operand. */
+export interface CallableFlowArgumentSite {
+    readonly kind: 'argument';
+    readonly callSite: Range;
+    readonly parameterIndex: number;
+    readonly source: CallableFlowOperand;
+    /** Direct callee spelling used when an earlier resolver already emitted the edge. */
+    readonly directCalleeName?: string;
+}
+export type CallableFlowInvocationKind = 'indirect' | 'member-pointer' | 'callable-object';
+/** A syntactically indirect invocation owned by callable-value-flow. */
+export interface CallableFlowInvokeSite {
+    readonly kind: 'invoke';
+    readonly callSite: Range;
+    readonly inScope: ScopeId;
+    readonly callee: CallableFlowOperand;
+    readonly receiver?: CallableFlowOperand;
+    readonly invocationKind: CallableFlowInvocationKind;
+    readonly arity?: number;
+}
+export type CallableFlowSite = CallableFlowSeedSite | CallableFlowCopySite | CallableFlowAliasSite | CallableFlowAddressSite | CallableFlowStoreSite | CallableFlowLoadSite | CallableFlowFormalSite | CallableFlowArgumentSite | CallableFlowInvokeSite;
+//# sourceMappingURL=callable-flow-site.d.ts.map

package/dist/_shared/scope-resolution/callable-flow-site.d.ts.map

@@ -0,0 +1 @@
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package/dist/_shared/scope-resolution/callable-flow-site.js

@@ -0,0 +1,11 @@
+/**
+ * Always-on callable-value-flow facts produced during scope extraction.
+ *
+ * These records deliberately contain no parser nodes or provider-private
+ * objects: they cross the worker, disk-cache, and ParsedFile-store boundaries.
+ * Language providers recognize syntax and emit `@callable-flow.*` captures;
+ * the central extractor attaches lexical scope ids and materializes this
+ * language-neutral representation.
+ */
+export {};
+//# sourceMappingURL=callable-flow-site.js.map

package/dist/_shared/scope-resolution/callable-flow-site.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"callable-flow-site.js","sourceRoot":"","sources":["../../src/scope-resolution/callable-flow-site.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG"}

package/dist/_shared/scope-resolution/finalize-algorithm.d.ts

@@ -83,7 +83,7 @@ export interface FinalizeHooks {
      * Return `null` when no target file is resolvable (e.g., `np.foo` when
      * `numpy` is external to the workspace).
      */
-    resolveImportTarget(targetRaw: string, fromFile: string, workspaceIndex: WorkspaceIndex): string | readonly string[] | null;
+    resolveImportTarget(targetRaw: string, fromFile: string, workspaceIndex: WorkspaceIndex, parsedImport?: ParsedImport): string | readonly string[] | null;
     /**
      * For a wildcard `import * from M`, return the names visible in the
      * exporting module scope `M`. The finalize pass looks each name up in

package/dist/_shared/scope-resolution/finalize-algorithm.d.ts.map

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