npm - gitnexus - Versions diffs - 1.6.10-rc.4 → 1.6.10-rc.41 - Mend

gitnexus 1.6.10-rc.4 → 1.6.10-rc.41

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (258) hide show

package/README.md CHANGED Viewed

@@ -163,6 +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:
@@ -223,7 +233,7 @@ gitnexus analyze --embeddings    # Enable embedding generation (slower, better s
 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
@@ -239,6 +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
@@ -273,10 +285,13 @@ 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_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.
+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
@@ -318,7 +333,7 @@ GitNexus ships with skill files that teach AI agents how to use the tools effect
 - **Guide** — GitNexus tool/resource/schema reference for the agent
 - **CLI** — Run analyze/status/clean/wiki commands on request
-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
@@ -448,13 +463,14 @@ GitNexus uses optional DuckDB extensions for BM25 and vector search. The `gitnex
 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 — 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_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.                                                                                                                                                                                                                                                                                                                                                                                                                |
 ```bash
 # Offline/airgapped: never reach the network for extensions
@@ -519,11 +535,13 @@ For repositories with very large source files, `GITNEXUS_WORKER_SUB_BATCH_MAX_BY
 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.
-| 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_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
@@ -535,17 +553,26 @@ 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/integrations/resilient-fetch.d.ts CHANGED Viewed

@@ -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;

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

@@ -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 CHANGED Viewed

	@@ -1 +1 @@
1	- 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1	+ 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package/dist/_shared/scope-resolution/finalize-algorithm.d.ts CHANGED Viewed

@@ -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 CHANGED Viewed

	@@ -1 +1 @@
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package/dist/_shared/scope-resolution/finalize-algorithm.js CHANGED Viewed

@@ -192,7 +192,7 @@ function makeEdgeDrafts(parsed, file, hooks, workspace) {
             },
         ];
     }
-    const targetFile = hooks.resolveImportTarget(parsed.targetRaw ?? '', file.filePath, workspace);
+    const targetFile = hooks.resolveImportTarget(parsed.targetRaw ?? '', file.filePath, workspace, parsed);
     // Edge is unresolvable at the file level — mark unresolved now.
     if (targetFile === null) {
         const base = {

package/dist/_shared/scope-resolution/finalize-algorithm.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/_shared/scope-resolution/types.d.ts CHANGED Viewed

@@ -85,6 +85,9 @@ export type ParsedImport =
     readonly localName: string;
     readonly importedName: string;
     readonly targetRaw: string;
+    /** Provider-specific imported symbol category when module and symbol
+     * namespaces have distinct resolution rules (for example PHP). */
+    readonly importedSymbolKind?: 'type' | 'function' | 'const';
     /**
      * Set by providers when `targetRaw` already names the imported symbol
      * rather than only its containing module. Consumers that compose
@@ -107,6 +110,8 @@ export type ParsedImport =
     readonly alias: string;
     readonly targetRaw: string;
     /** See the same field on the `named` variant. */
+    readonly importedSymbolKind?: 'type' | 'function' | 'const';
+    /** See the same field on the `named` variant. */
     readonly targetIncludesImportedName?: boolean;
 }
 /**

package/dist/_shared/scope-resolution/types.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/cli/ai-context.js CHANGED Viewed

@@ -81,22 +81,22 @@ export function generateGitNexusContent(projectName, stats, opts = {}) {
     const { generatedSkills, groupNames, noStats, skipSkills, runnerPath = '.gitnexus/run.cjs', defaultBranch = 'main', hasPdg = false, } = opts;
     const generatedRows = generatedSkills && generatedSkills.length > 0
         ? generatedSkills
-            .map((s) => `| Work in the ${s.label} area (${s.symbolCount} symbols) | \`.claude/skills/generated/${s.name}/SKILL.md\` |`)
+            .map((s) => `| Work in the ${s.label} area (${s.symbolCount} symbols) | \`.claude/skills/${s.name}/SKILL.md\` |`)
             .join('\n')
         : '';
     // Standard skill rows reference files installed by installSkills(). When
     // --skip-skills suppresses that install, these rows must be omitted — else
     // AGENTS.md/CLAUDE.md would direct agents to read files that don't exist.
-    // Community skills (generatedRows) live in .claude/skills/generated/ and
+    // Community skills (generatedRows) live directly under .claude/skills/ and
     // are independent of --skip-skills, so they remain when present.
     const standardSkillsRows = skipSkills
         ? ''
-        : `| Understand architecture / "How does X work?" | \`.claude/skills/gitnexus/gitnexus-exploring/SKILL.md\` |
-| Blast radius / "What breaks if I change X?" | \`.claude/skills/gitnexus/gitnexus-impact-analysis/SKILL.md\` |
-| Trace bugs / "Why is X failing?" | \`.claude/skills/gitnexus/gitnexus-debugging/SKILL.md\` |
-| Rename / extract / split / refactor | \`.claude/skills/gitnexus/gitnexus-refactoring/SKILL.md\` |
-| Tools, resources, schema reference | \`.claude/skills/gitnexus/gitnexus-guide/SKILL.md\` |
-| Index, status, clean, wiki CLI commands | \`.claude/skills/gitnexus/gitnexus-cli/SKILL.md\` |`;
+        : `| Understand architecture / "How does X work?" | \`.claude/skills/gitnexus-exploring/SKILL.md\` |
+| Blast radius / "What breaks if I change X?" | \`.claude/skills/gitnexus-impact-analysis/SKILL.md\` |
+| Trace bugs / "Why is X failing?" | \`.claude/skills/gitnexus-debugging/SKILL.md\` |
+| Rename / extract / split / refactor | \`.claude/skills/gitnexus-refactoring/SKILL.md\` |
+| Tools, resources, schema reference | \`.claude/skills/gitnexus-guide/SKILL.md\` |
+| Index, status, clean, wiki CLI commands | \`.claude/skills/gitnexus-cli/SKILL.md\` |`;
     const tableBody = [standardSkillsRows, generatedRows].filter(Boolean).join('\n');
     const skillsTable = tableBody
         ? `| Task | Read this skill file |
@@ -253,11 +253,12 @@ async function upsertGitNexusSection(filePath, content, projectName, stats, noSt
     return 'appended';
 }
 /**
- * Install GitNexus skills to .claude/skills/gitnexus/
+ * Install GitNexus skills as direct children of .claude/skills/
  * Works natively with Claude Code, Cursor, and GitHub Copilot
  */
 async function installSkills(repoPath) {
-    const skillsDir = path.join(repoPath, '.claude', 'skills', 'gitnexus');
+    const skillsDir = path.join(repoPath, '.claude', 'skills');
+    const legacySkillsDir = path.join(skillsDir, 'gitnexus');
     const installedSkills = [];
     // Skill definitions bundled with the package
     const skills = [
@@ -314,6 +315,15 @@ Use GitNexus tools to accomplish this task.
             }
             await fs.writeFile(skillPath, skillContent, 'utf-8');
             installedSkills.push(skill.name);
+            // Previous releases installed these known standard skills one level too
+            // deep. Remove only the child owned by this installer; unknown siblings
+            // under the legacy grouping directory may be user-authored and survive.
+            try {
+                await fs.rm(path.join(legacySkillsDir, skill.name), { recursive: true, force: true });
+            }
+            catch (err) {
+                logger.warn({ err }, `Warning: Could not remove legacy skill ${skill.name}:`);
+            }
         }
         catch (err) {
             // Skip on error, don't fail the whole process
@@ -366,15 +376,15 @@ export async function generateAIContextFiles(repoPath, storagePath, projectName,
         createdFiles.push('AGENTS.md (skipped via --skip-agents-md)');
         createdFiles.push('CLAUDE.md (skipped via --skip-agents-md)');
     }
-    // Install skills to .claude/skills/gitnexus/ (unless --skip-skills)
+    // Install standard skills directly under .claude/skills/ (unless --skip-skills)
     if (!options?.skipSkills) {
         const installedSkills = await installSkills(repoPath);
         if (installedSkills.length > 0) {
-            createdFiles.push(`.claude/skills/gitnexus/ (${installedSkills.length} skills)`);
+            createdFiles.push(`.claude/skills/gitnexus-*/ (${installedSkills.length} skills)`);
         }
     }
     else {
-        createdFiles.push('.claude/skills/gitnexus/ (skipped via --skip-skills)');
+        createdFiles.push('.claude/skills/gitnexus-*/ (skipped via --skip-skills)');
     }
     return { files: createdFiles };
 }

package/dist/cli/analyze.d.ts CHANGED Viewed

@@ -55,7 +55,7 @@ export interface AnalyzeOptions {
      * default-on case.
      */
     stats?: boolean;
-    /** Skip installing standard GitNexus skill files to .claude/skills/gitnexus/. */
+    /** Skip installing standard GitNexus skill files directly under .claude/skills/. */
     skipSkills?: boolean;
     /**
      * Default branch for the generated regression-compare example (#243). From