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7 changes: 2 additions & 5 deletions .claude/skills/gitnexus/gitnexus-cli/SKILL.md
Original file line number Diff line number Diff line change
@@ -1,7 +1,4 @@
---
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\""
---
<!-- AUTO-GENERATED FROM gitnexus/skills/gitnexus-cli.md — DO NOT EDIT -->

# GitNexus CLI Commands

Expand All @@ -22,7 +19,7 @@ Run from the project root. This parses all source files, builds the knowledge gr
| `--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.
**When to run:** First time in a project, after major code changes, or when `gitnexus://repo/{name}/context` reports the index is stale. In Claude Code, a PostToolUse hook runs `analyze` automatically after `git commit` and `git merge`, preserving embeddings if previously generated.

### status — Check index freshness

Expand Down
175 changes: 86 additions & 89 deletions .claude/skills/gitnexus/gitnexus-debugging/SKILL.md
Original file line number Diff line number Diff line change
@@ -1,89 +1,86 @@
---
name: gitnexus-debugging
description: "Use when the user is debugging a bug, tracing an error, or asking why something fails. Examples: \"Why is X failing?\", \"Where does this error come from?\", \"Trace this bug\""
---

# Debugging with GitNexus

## When to Use

- "Why is this function failing?"
- "Trace where this error comes from"
- "Who calls this method?"
- "This endpoint returns 500"
- Investigating bugs, errors, or unexpected behavior

## Workflow

```
1. gitnexus_query({query: "<error or symptom>"}) → Find related execution flows
2. gitnexus_context({name: "<suspect>"}) → See callers/callees/processes
3. READ gitnexus://repo/{name}/process/{name} → Trace execution flow
4. gitnexus_cypher({query: "MATCH path..."}) → Custom traces if needed
```

> If "Index is stale" → run `npx gitnexus analyze` in terminal.

## Checklist

```
- [ ] Understand the symptom (error message, unexpected behavior)
- [ ] gitnexus_query for error text or related code
- [ ] Identify the suspect function from returned processes
- [ ] gitnexus_context to see callers and callees
- [ ] Trace execution flow via process resource if applicable
- [ ] gitnexus_cypher for custom call chain traces if needed
- [ ] Read source files to confirm root cause
```

## Debugging Patterns

| Symptom | GitNexus Approach |
| -------------------- | ---------------------------------------------------------- |
| Error message | `gitnexus_query` for error text → `context` on throw sites |
| Wrong return value | `context` on the function → trace callees for data flow |
| Intermittent failure | `context` → look for external calls, async deps |
| Performance issue | `context` → find symbols with many callers (hot paths) |
| Recent regression | `detect_changes` to see what your changes affect |

## Tools

**gitnexus_query** — find code related to error:

```
gitnexus_query({query: "payment validation error"})
→ Processes: CheckoutFlow, ErrorHandling
→ Symbols: validatePayment, handlePaymentError, PaymentException
```

**gitnexus_context** — full context for a suspect:

```
gitnexus_context({name: "validatePayment"})
→ Incoming calls: processCheckout, webhookHandler
→ Outgoing calls: verifyCard, fetchRates (external API!)
→ Processes: CheckoutFlow (step 3/7)
```

**gitnexus_cypher** — custom call chain traces:

```cypher
MATCH path = (a)-[:CodeRelation {type: 'CALLS'}*1..2]->(b:Function {name: "validatePayment"})
RETURN [n IN nodes(path) | n.name] AS chain
```

## Example: "Payment endpoint returns 500 intermittently"

```
1. gitnexus_query({query: "payment error handling"})
→ Processes: CheckoutFlow, ErrorHandling
→ Symbols: validatePayment, handlePaymentError

2. gitnexus_context({name: "validatePayment"})
→ Outgoing calls: verifyCard, fetchRates (external API!)

3. READ gitnexus://repo/my-app/process/CheckoutFlow
→ Step 3: validatePayment → calls fetchRates (external)

4. Root cause: fetchRates calls external API without proper timeout
```
<!-- AUTO-GENERATED FROM gitnexus/skills/gitnexus-debugging.md — DO NOT EDIT -->

# Debugging with GitNexus

## When to Use

- "Why is this function failing?"
- "Trace where this error comes from"
- "Who calls this method?"
- "This endpoint returns 500"
- Investigating bugs, errors, or unexpected behavior

## Workflow

```
1. gitnexus_query({query: "<error or symptom>"}) → Find related execution flows
2. gitnexus_context({name: "<suspect>"}) → See callers/callees/processes
3. READ gitnexus://repo/{name}/process/{name} → Trace execution flow
4. gitnexus_cypher({query: "MATCH path..."}) → Custom traces if needed
```
Comment on lines +15 to +20

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⚠️ Potential issue | 🟡 Minor

Add explicit fence languages in the generated markdown.

These unlabeled fenced blocks trigger markdownlint MD040 repeatedly. Since this file is auto-generated, please fix the canonical skill source or sync step to emit languages like text, bash, or cypher instead of patching the derived file directly.

Also applies to: 26-34, 50-54, 58-63, 74-86

🧰 Tools
🪛 markdownlint-cli2 (0.21.0)

[warning] 15-15: Fenced code blocks should have a language specified

(MD040, fenced-code-language)

🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed.

In @.claude/skills/gitnexus/gitnexus-debugging/SKILL.md around lines 15 - 20,
The markdown generator is emitting unlabeled fenced code blocks (examples show
backtick blocks containing gitnexus_query, gitnexus_context, READ
gitnexus://repo/... and gitnexus_cypher) which triggers MD040; update the
canonical skill source or the sync/export step that renders SKILL.md so that
every fenced block includes an explicit language hint (e.g., ```text for plain
examples, ```bash for shell snippets, ```cypher for cypher queries) rather than
unlabeled ```; ensure the change affects all similar blocks (the ones containing
gitnexus_query, gitnexus_context, READ gitnexus://repo/... and gitnexus_cypher)
so the generated file no longer contains unlabeled fences.


> If "Index is stale" → run `npx gitnexus analyze` in terminal.

## Checklist

```
- [ ] Understand the symptom (error message, unexpected behavior)
- [ ] gitnexus_query for error text or related code
- [ ] Identify the suspect function from returned processes
- [ ] gitnexus_context to see callers and callees
- [ ] Trace execution flow via process resource if applicable
- [ ] gitnexus_cypher for custom call chain traces if needed
- [ ] Read source files to confirm root cause
```

## Debugging Patterns

| Symptom | GitNexus Approach |
| -------------------- | ---------------------------------------------------------- |
| Error message | `gitnexus_query` for error text → `context` on throw sites |
| Wrong return value | `context` on the function → trace callees for data flow |
| Intermittent failure | `context` → look for external calls, async deps |
| Performance issue | `context` → find symbols with many callers (hot paths) |
| Recent regression | `detect_changes` to see what your changes affect |

## Tools

**gitnexus_query** — find code related to error:

```
gitnexus_query({query: "payment validation error"})
→ Processes: CheckoutFlow, ErrorHandling
→ Symbols: validatePayment, handlePaymentError, PaymentException
```

**gitnexus_context** — full context for a suspect:

```
gitnexus_context({name: "validatePayment"})
→ Incoming calls: processCheckout, webhookHandler
→ Outgoing calls: verifyCard, fetchRates (external API!)
→ Processes: CheckoutFlow (step 3/7)
```

**gitnexus_cypher** — custom call chain traces:

```cypher
MATCH path = (a)-[:CodeRelation {type: 'CALLS'}*1..2]->(b:Function {name: "validatePayment"})
RETURN [n IN nodes(path) | n.name] AS chain
```

## Example: "Payment endpoint returns 500 intermittently"

```
1. gitnexus_query({query: "payment error handling"})
→ Processes: CheckoutFlow, ErrorHandling
→ Symbols: validatePayment, handlePaymentError

2. gitnexus_context({name: "validatePayment"})
→ Outgoing calls: verifyCard, fetchRates (external API!)

3. READ gitnexus://repo/my-app/process/CheckoutFlow
→ Step 3: validatePayment → calls fetchRates (external)

4. Root cause: fetchRates calls external API without proper timeout
```
153 changes: 75 additions & 78 deletions .claude/skills/gitnexus/gitnexus-exploring/SKILL.md
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@@ -1,78 +1,75 @@
---
name: gitnexus-exploring
description: "Use when the user asks how code works, wants to understand architecture, trace execution flows, or explore unfamiliar parts of the codebase. Examples: \"How does X work?\", \"What calls this function?\", \"Show me the auth flow\""
---

# Exploring Codebases with GitNexus

## When to Use

- "How does authentication work?"
- "What's the project structure?"
- "Show me the main components"
- "Where is the database logic?"
- Understanding code you haven't seen before

## Workflow

```
1. READ gitnexus://repos → Discover indexed repos
2. READ gitnexus://repo/{name}/context → Codebase overview, check staleness
3. gitnexus_query({query: "<what you want to understand>"}) → Find related execution flows
4. gitnexus_context({name: "<symbol>"}) → Deep dive on specific symbol
5. READ gitnexus://repo/{name}/process/{name} → Trace full execution flow
```

> If step 2 says "Index is stale" → run `npx gitnexus analyze` in terminal.

## Checklist

```
- [ ] READ gitnexus://repo/{name}/context
- [ ] gitnexus_query for the concept you want to understand
- [ ] Review returned processes (execution flows)
- [ ] gitnexus_context on key symbols for callers/callees
- [ ] READ process resource for full execution traces
- [ ] Read source files for implementation details
```

## Resources

| Resource | What you get |
| --------------------------------------- | ------------------------------------------------------- |
| `gitnexus://repo/{name}/context` | Stats, staleness warning (~150 tokens) |
| `gitnexus://repo/{name}/clusters` | All functional areas with cohesion scores (~300 tokens) |
| `gitnexus://repo/{name}/cluster/{name}` | Area members with file paths (~500 tokens) |
| `gitnexus://repo/{name}/process/{name}` | Step-by-step execution trace (~200 tokens) |

## Tools

**gitnexus_query** — find execution flows related to a concept:

```
gitnexus_query({query: "payment processing"})
→ Processes: CheckoutFlow, RefundFlow, WebhookHandler
→ Symbols grouped by flow with file locations
```

**gitnexus_context** — 360-degree view of a symbol:

```
gitnexus_context({name: "validateUser"})
→ Incoming calls: loginHandler, apiMiddleware
→ Outgoing calls: checkToken, getUserById
→ Processes: LoginFlow (step 2/5), TokenRefresh (step 1/3)
```

## Example: "How does payment processing work?"

```
1. READ gitnexus://repo/my-app/context → 918 symbols, 45 processes
2. gitnexus_query({query: "payment processing"})
→ CheckoutFlow: processPayment → validateCard → chargeStripe
→ RefundFlow: initiateRefund → calculateRefund → processRefund
3. gitnexus_context({name: "processPayment"})
→ Incoming: checkoutHandler, webhookHandler
→ Outgoing: validateCard, chargeStripe, saveTransaction
4. Read src/payments/processor.ts for implementation details
```
<!-- AUTO-GENERATED FROM gitnexus/skills/gitnexus-exploring.md — DO NOT EDIT -->

# Exploring Codebases with GitNexus

## When to Use

- "How does authentication work?"
- "What's the project structure?"
- "Show me the main components"
- "Where is the database logic?"
- Understanding code you haven't seen before

## Workflow

```
1. READ gitnexus://repos → Discover indexed repos
2. READ gitnexus://repo/{name}/context → Codebase overview, check staleness
3. gitnexus_query({query: "<what you want to understand>"}) → Find related execution flows
4. gitnexus_context({name: "<symbol>"}) → Deep dive on specific symbol
5. READ gitnexus://repo/{name}/process/{name} → Trace full execution flow
```

> If step 2 says "Index is stale" → run `npx gitnexus analyze` in terminal.

## Checklist

```
- [ ] READ gitnexus://repo/{name}/context
- [ ] gitnexus_query for the concept you want to understand
- [ ] Review returned processes (execution flows)
- [ ] gitnexus_context on key symbols for callers/callees
- [ ] READ process resource for full execution traces
- [ ] Read source files for implementation details
```

## Resources

| Resource | What you get |
| --------------------------------------- | ------------------------------------------------------- |
| `gitnexus://repo/{name}/context` | Stats, staleness warning (~150 tokens) |
| `gitnexus://repo/{name}/clusters` | All functional areas with cohesion scores (~300 tokens) |
| `gitnexus://repo/{name}/cluster/{name}` | Area members with file paths (~500 tokens) |
| `gitnexus://repo/{name}/process/{name}` | Step-by-step execution trace (~200 tokens) |

## Tools

**gitnexus_query** — find execution flows related to a concept:

```
gitnexus_query({query: "payment processing"})
→ Processes: CheckoutFlow, RefundFlow, WebhookHandler
→ Symbols grouped by flow with file locations
```

**gitnexus_context** — 360-degree view of a symbol:

```
gitnexus_context({name: "validateUser"})
→ Incoming calls: loginHandler, apiMiddleware
→ Outgoing calls: checkToken, getUserById
→ Processes: LoginFlow (step 2/5), TokenRefresh (step 1/3)
```

## Example: "How does payment processing work?"

```
1. READ gitnexus://repo/my-app/context → 918 symbols, 45 processes
2. gitnexus_query({query: "payment processing"})
→ CheckoutFlow: processPayment → validateCard → chargeStripe
→ RefundFlow: initiateRefund → calculateRefund → processRefund
3. gitnexus_context({name: "processPayment"})
→ Incoming: checkoutHandler, webhookHandler
→ Outgoing: validateCard, chargeStripe, saveTransaction
4. Read src/payments/processor.ts for implementation details
```
5 changes: 1 addition & 4 deletions .claude/skills/gitnexus/gitnexus-guide/SKILL.md
Original file line number Diff line number Diff line change
@@ -1,7 +1,4 @@
---
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?\""
---
<!-- AUTO-GENERATED FROM gitnexus/skills/gitnexus-guide.md — DO NOT EDIT -->

# GitNexus Guide

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