Skip to content

Refactor skill installation to setup with dynamic discovery #4

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Closed
L1nusB wants to merge 15 commits into from
Closed

Refactor skill installation to setup with dynamic discovery #4

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
15 commits
Select commit Hold shift + click to select a range
ebfd312
chore: run basic commands
L1nusB Mar 7, 2026
02eb465
docs: create initial summary and tracking document
L1nusB Mar 7, 2026
b246c87
test: add test suite for skill installation refactor
L1nusB Mar 7, 2026
c3f6995
test(skills): activate pre-refactor acceptance suite
L1nusB Mar 7, 2026
c2ffb76
refactor: unify skill installation in setup, remove from analyze
L1nusB Mar 7, 2026
f15b0aa
fix(skills): cover worktree cleanup and no-op analyze notice
L1nusB Mar 7, 2026
c0f12a8
docs: update README to reflect skill installation changes
L1nusB Mar 7, 2026
e132f77
docs: plan auto-discovery of skill names from disk
L1nusB Mar 7, 2026
4a88ff6
test: add acceptance tests for discoverSkillNames (#27-33)
L1nusB Mar 7, 2026
011b2c1
feat(skills): auto-discover skill names from disk
L1nusB Mar 7, 2026
70a9f03
docs: add pr description
L1nusB Mar 7, 2026
2fa3dd1
test(skills): add discovery edge-case coverage
L1nusB Mar 7, 2026
774ac8f
fix(skills): address review feedback — guard cleanup, fix README count
L1nusB Mar 7, 2026
0e7301d
docs: update pr description
L1nusB Mar 7, 2026
2920f07
chore: address review nitpicks — docs, unused variable
L1nusB Mar 7, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
164 changes: 82 additions & 82 deletions .claude/skills/gitnexus/gitnexus-cli/SKILL.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,82 +1,82 @@
---
name: gitnexus-cli
description: "Use when the user needs to run GitNexus CLI commands like analyze/index a repo, check status, clean the index, generate a wiki, or list indexed repos. Examples: \"Index this repo\", \"Reanalyze the codebase\", \"Generate a wiki\""
---

# GitNexus CLI Commands

All commands work via `npx` — no global install required.

## Commands

### analyze — Build or refresh the index

```bash
npx gitnexus analyze
```

Run from the project root. This parses all source files, builds the knowledge graph, writes it to `.gitnexus/`, and generates CLAUDE.md / AGENTS.md context files.

| Flag | Effect |
| -------------- | ---------------------------------------------------------------- |
| `--force` | Force full re-index even if up to date |
| `--embeddings` | Enable embedding generation for semantic search (off by default) |

**When to run:** First time in a project, after major code changes, or when `gitnexus://repo/{name}/context` reports the index is stale.

### status — Check index freshness

```bash
npx gitnexus status
```

Shows whether the current repo has a GitNexus index, when it was last updated, and symbol/relationship counts. Use this to check if re-indexing is needed.

### clean — Delete the index

```bash
npx gitnexus clean
```

Deletes the `.gitnexus/` directory and unregisters the repo from the global registry. Use before re-indexing if the index is corrupt or after removing GitNexus from a project.

| Flag | Effect |
| --------- | ------------------------------------------------- |
| `--force` | Skip confirmation prompt |
| `--all` | Clean all indexed repos, not just the current one |

### wiki — Generate documentation from the graph

```bash
npx gitnexus wiki
```

Generates repository documentation from the knowledge graph using an LLM. Requires an API key (saved to `~/.gitnexus/config.json` on first use).

| Flag | Effect |
| ------------------- | ----------------------------------------- |
| `--force` | Force full regeneration |
| `--model <model>` | LLM model (default: minimax/minimax-m2.5) |
| `--base-url <url>` | LLM API base URL |
| `--api-key <key>` | LLM API key |
| `--concurrency <n>` | Parallel LLM calls (default: 3) |
| `--gist` | Publish wiki as a public GitHub Gist |

### list — Show all indexed repos

```bash
npx gitnexus list
```

Lists all repositories registered in `~/.gitnexus/registry.json`. The MCP `list_repos` tool provides the same information.

## After Indexing

1. **Read `gitnexus://repo/{name}/context`** to verify the index loaded
2. Use the other GitNexus skills (`exploring`, `debugging`, `impact-analysis`, `refactoring`) for your task

## Troubleshooting

- **"Not inside a git repository"**: Run from a directory inside a git repo
- **Index is stale after re-analyzing**: Restart Claude Code to reload the MCP server
- **Embeddings slow**: Omit `--embeddings` (it's off by default) or set `OPENAI_API_KEY` for faster API-based embedding
---
name: gitnexus-cli
description: "Use when the user needs to run GitNexus CLI commands like analyze/index a repo, check status, clean the index, generate a wiki, or list indexed repos. Examples: \"Index this repo\", \"Reanalyze the codebase\", \"Generate a wiki\""
---
# GitNexus CLI Commands
All commands work via `npx` — no global install required.
## Commands
### analyze — Build or refresh the index
```bash
npx gitnexus analyze
```
Run from the project root. This parses all source files, builds the knowledge graph, writes it to `.gitnexus/`, and generates CLAUDE.md / AGENTS.md context files.
| Flag | Effect |
| -------------- | ---------------------------------------------------------------- |
| `--force` | Force full re-index even if up to date |
| `--embeddings` | Enable embedding generation for semantic search (off by default) |
**When to run:** First time in a project, after major code changes, or when `gitnexus://repo/{name}/context` reports the index is stale.
### status — Check index freshness
```bash
npx gitnexus status
```
Shows whether the current repo has a GitNexus index, when it was last updated, and symbol/relationship counts. Use this to check if re-indexing is needed.
### clean — Delete the index
```bash
npx gitnexus clean
```
Deletes the `.gitnexus/` directory and unregisters the repo from the global registry. Use before re-indexing if the index is corrupt or after removing GitNexus from a project.
| Flag | Effect |
| --------- | ------------------------------------------------- |
| `--force` | Skip confirmation prompt |
| `--all` | Clean all indexed repos, not just the current one |
### wiki — Generate documentation from the graph
```bash
npx gitnexus wiki
```
Generates repository documentation from the knowledge graph using an LLM. Requires an API key (saved to `~/.gitnexus/config.json` on first use).
| Flag | Effect |
| ------------------- | ----------------------------------------- |
| `--force` | Force full regeneration |
| `--model <model>` | LLM model (default: minimax/minimax-m2.5) |
| `--base-url <url>` | LLM API base URL |
| `--api-key <key>` | LLM API key |
| `--concurrency <n>` | Parallel LLM calls (default: 3) |
| `--gist` | Publish wiki as a public GitHub Gist |
### list — Show all indexed repos
```bash
npx gitnexus list
```
Lists all repositories registered in `~/.gitnexus/registry.json`. The MCP `list_repos` tool provides the same information.
## After Indexing
1. **Read `gitnexus://repo/{name}/context`** to verify the index loaded
2. Use the other GitNexus skills (`exploring`, `debugging`, `impact-analysis`, `refactoring`) for your task
## Troubleshooting
- **"Not inside a git repository"**: Run from a directory inside a git repo
- **Index is stale after re-analyzing**: Restart Claude Code to reload the MCP server
- **Embeddings slow**: Omit `--embeddings` (it's off by default) or set `OPENAI_API_KEY` for faster API-based embedding
128 changes: 64 additions & 64 deletions .claude/skills/gitnexus/gitnexus-guide/SKILL.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,64 +1,64 @@
---
name: gitnexus-guide
description: "Use when the user asks about GitNexus itself — available tools, how to query the knowledge graph, MCP resources, graph schema, or workflow reference. Examples: \"What GitNexus tools are available?\", \"How do I use GitNexus?\""
---

# GitNexus Guide

Quick reference for all GitNexus MCP tools, resources, and the knowledge graph schema.

## Always Start Here

For any task involving code understanding, debugging, impact analysis, or refactoring:

1. **Read `gitnexus://repo/{name}/context`** — codebase overview + check index freshness
2. **Match your task to a skill below** and **read that skill file**
3. **Follow the skill's workflow and checklist**

> If step 1 warns the index is stale, run `npx gitnexus analyze` in the terminal first.

## Skills

| Task | Skill to read |
| -------------------------------------------- | ------------------- |
| Understand architecture / "How does X work?" | `gitnexus-exploring` |
| Blast radius / "What breaks if I change X?" | `gitnexus-impact-analysis` |
| Trace bugs / "Why is X failing?" | `gitnexus-debugging` |
| Rename / extract / split / refactor | `gitnexus-refactoring` |
| Tools, resources, schema reference | `gitnexus-guide` (this file) |
| Index, status, clean, wiki CLI commands | `gitnexus-cli` |

## Tools Reference

| Tool | What it gives you |
| ---------------- | ------------------------------------------------------------------------ |
| `query` | Process-grouped code intelligence — execution flows related to a concept |
| `context` | 360-degree symbol view — categorized refs, processes it participates in |
| `impact` | Symbol blast radius — what breaks at depth 1/2/3 with confidence |
| `detect_changes` | Git-diff impact — what do your current changes affect |
| `rename` | Multi-file coordinated rename with confidence-tagged edits |
| `cypher` | Raw graph queries (read `gitnexus://repo/{name}/schema` first) |
| `list_repos` | Discover indexed repos |

## Resources Reference

Lightweight reads (~100-500 tokens) for navigation:

| Resource | Content |
| ---------------------------------------------- | ----------------------------------------- |
| `gitnexus://repo/{name}/context` | Stats, staleness check |
| `gitnexus://repo/{name}/clusters` | All functional areas with cohesion scores |
| `gitnexus://repo/{name}/cluster/{clusterName}` | Area members |
| `gitnexus://repo/{name}/processes` | All execution flows |
| `gitnexus://repo/{name}/process/{processName}` | Step-by-step trace |
| `gitnexus://repo/{name}/schema` | Graph schema for Cypher |

## Graph Schema

**Nodes:** File, Function, Class, Interface, Method, Community, Process
**Edges (via CodeRelation.type):** CALLS, IMPORTS, EXTENDS, IMPLEMENTS, DEFINES, MEMBER_OF, STEP_IN_PROCESS

```cypher
MATCH (caller)-[:CodeRelation {type: 'CALLS'}]->(f:Function {name: "myFunc"})
RETURN caller.name, caller.filePath
```
---
name: gitnexus-guide
description: "Use when the user asks about GitNexus itself — available tools, how to query the knowledge graph, MCP resources, graph schema, or workflow reference. Examples: \"What GitNexus tools are available?\", \"How do I use GitNexus?\""
---
# GitNexus Guide
Quick reference for all GitNexus MCP tools, resources, and the knowledge graph schema.
## Always Start Here
For any task involving code understanding, debugging, impact analysis, or refactoring:
1. **Read `gitnexus://repo/{name}/context`** — codebase overview + check index freshness
2. **Match your task to a skill below** and **read that skill file**
3. **Follow the skill's workflow and checklist**
> If step 1 warns the index is stale, run `npx gitnexus analyze` in the terminal first.
## Skills
| Task | Skill to read |
| -------------------------------------------- | ------------------- |
| Understand architecture / "How does X work?" | `gitnexus-exploring` |
| Blast radius / "What breaks if I change X?" | `gitnexus-impact-analysis` |
| Trace bugs / "Why is X failing?" | `gitnexus-debugging` |
| Rename / extract / split / refactor | `gitnexus-refactoring` |
| Tools, resources, schema reference | `gitnexus-guide` (this file) |
| Index, status, clean, wiki CLI commands | `gitnexus-cli` |
## Tools Reference
| Tool | What it gives you |
| ---------------- | ------------------------------------------------------------------------ |
| `query` | Process-grouped code intelligence — execution flows related to a concept |
| `context` | 360-degree symbol view — categorized refs, processes it participates in |
| `impact` | Symbol blast radius — what breaks at depth 1/2/3 with confidence |
| `detect_changes` | Git-diff impact — what do your current changes affect |
| `rename` | Multi-file coordinated rename with confidence-tagged edits |
| `cypher` | Raw graph queries (read `gitnexus://repo/{name}/schema` first) |
| `list_repos` | Discover indexed repos |
## Resources Reference
Lightweight reads (~100-500 tokens) for navigation:
| Resource | Content |
| ---------------------------------------------- | ----------------------------------------- |
| `gitnexus://repo/{name}/context` | Stats, staleness check |
| `gitnexus://repo/{name}/clusters` | All functional areas with cohesion scores |
| `gitnexus://repo/{name}/cluster/{clusterName}` | Area members |
| `gitnexus://repo/{name}/processes` | All execution flows |
| `gitnexus://repo/{name}/process/{processName}` | Step-by-step trace |
| `gitnexus://repo/{name}/schema` | Graph schema for Cypher |
## Graph Schema
**Nodes:** File, Function, Class, Interface, Method, Community, Process
**Edges (via CodeRelation.type):** CALLS, IMPORTS, EXTENDS, IMPLEMENTS, DEFINES, MEMBER_OF, STEP_IN_PROCESS
```cypher
MATCH (caller)-[:CodeRelation {type: 'CALLS'}]->(f:Function {name: "myFunc"})
RETURN caller.name, caller.filePath
```
12 changes: 6 additions & 6 deletions AGENTS.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
<!-- gitnexus:start -->
# GitNexus — Code Intelligence

This project is indexed by GitNexus as **GitNexus** (1573 symbols, 4146 relationships, 120 execution flows). Use the GitNexus MCP tools to understand code, assess impact, and navigate safely.
This project is indexed by GitNexus as **intelligent_skills** (1617 symbols, 4272 relationships, 123 execution flows). Use the GitNexus MCP tools to understand code, assess impact, and navigate safely.

> If any GitNexus tool warns the index is stale, run `npx gitnexus analyze` in terminal first.

Expand All @@ -17,7 +17,7 @@ This project is indexed by GitNexus as **GitNexus** (1573 symbols, 4146 relation

1. `gitnexus_query({query: "<error or symptom>"})` — find execution flows related to the issue
2. `gitnexus_context({name: "<suspect function>"})` — see all callers, callees, and process participation
3. `READ gitnexus://repo/GitNexus/process/{processName}` — trace the full execution flow step by step
3. `READ gitnexus://repo/intelligent_skills/process/{processName}` — trace the full execution flow step by step
4. For regressions: `gitnexus_detect_changes({scope: "compare", base_ref: "main"})` — see what your branch changed

## When Refactoring
Expand Down Expand Up @@ -56,10 +56,10 @@ This project is indexed by GitNexus as **GitNexus** (1573 symbols, 4146 relation

| Resource | Use for |
|----------|---------|
| `gitnexus://repo/GitNexus/context` | Codebase overview, check index freshness |
| `gitnexus://repo/GitNexus/clusters` | All functional areas |
| `gitnexus://repo/GitNexus/processes` | All execution flows |
| `gitnexus://repo/GitNexus/process/{name}` | Step-by-step execution trace |
| `gitnexus://repo/intelligent_skills/context` | Codebase overview, check index freshness |
| `gitnexus://repo/intelligent_skills/clusters` | All functional areas |
| `gitnexus://repo/intelligent_skills/processes` | All execution flows |
| `gitnexus://repo/intelligent_skills/process/{name}` | Step-by-step execution trace |

## Self-Check Before Finishing

Expand Down
12 changes: 6 additions & 6 deletions CLAUDE.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
<!-- gitnexus:start -->
# GitNexus — Code Intelligence

This project is indexed by GitNexus as **GitNexus** (1573 symbols, 4146 relationships, 120 execution flows). Use the GitNexus MCP tools to understand code, assess impact, and navigate safely.
This project is indexed by GitNexus as **intelligent_skills** (1617 symbols, 4272 relationships, 123 execution flows). Use the GitNexus MCP tools to understand code, assess impact, and navigate safely.

> If any GitNexus tool warns the index is stale, run `npx gitnexus analyze` in terminal first.

Expand All @@ -17,7 +17,7 @@ This project is indexed by GitNexus as **GitNexus** (1573 symbols, 4146 relation

1. `gitnexus_query({query: "<error or symptom>"})` — find execution flows related to the issue
2. `gitnexus_context({name: "<suspect function>"})` — see all callers, callees, and process participation
3. `READ gitnexus://repo/GitNexus/process/{processName}` — trace the full execution flow step by step
3. `READ gitnexus://repo/intelligent_skills/process/{processName}` — trace the full execution flow step by step
4. For regressions: `gitnexus_detect_changes({scope: "compare", base_ref: "main"})` — see what your branch changed

## When Refactoring
Expand Down Expand Up @@ -56,10 +56,10 @@ This project is indexed by GitNexus as **GitNexus** (1573 symbols, 4146 relation

| Resource | Use for |
|----------|---------|
| `gitnexus://repo/GitNexus/context` | Codebase overview, check index freshness |
| `gitnexus://repo/GitNexus/clusters` | All functional areas |
| `gitnexus://repo/GitNexus/processes` | All execution flows |
| `gitnexus://repo/GitNexus/process/{name}` | Step-by-step execution trace |
| `gitnexus://repo/intelligent_skills/context` | Codebase overview, check index freshness |
| `gitnexus://repo/intelligent_skills/clusters` | All functional areas |
| `gitnexus://repo/intelligent_skills/processes` | All execution flows |
| `gitnexus://repo/intelligent_skills/process/{name}` | Step-by-step execution trace |

## Self-Check Before Finishing

Expand Down
Loading