docs(skills): document installed GitNexus CLI usage

gitnexus/skills/gitnexus-cli.md

@@ -5,14 +5,14 @@ description: "Use when the user needs to run GitNexus CLI commands like analyze/
 
 # GitNexus CLI Commands
 
-All commands work via `npx` — no global install required.
+Commands below use the installed `gitnexus` CLI. If the CLI is not installed, use the equivalent `npx gitnexus ...` invocation.
 
 ## Commands
 
 ### analyze — Build or refresh the index
 
 ```bash
-npx gitnexus analyze
+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.
@@ -28,7 +28,7 @@ Run from the project root. This parses all source files, builds the knowledge gr
 ### status — Check index freshness
 
 ```bash
-npx gitnexus status
+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.
@@ -36,7 +36,7 @@ Shows whether the current repo has a GitNexus index, when it was last updated, a
 ### clean — Delete the index
 
 ```bash
-npx gitnexus clean
+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.
@@ -49,7 +49,7 @@ Deletes the `.gitnexus/` directory and unregisters the repo from the global regi
 ### wiki — Generate documentation from the graph
 
 ```bash
-npx gitnexus wiki
+gitnexus wiki
 ```
 
 Generates repository documentation from the knowledge graph using an LLM. Requires an API key (saved to `~/.gitnexus/config.json` on first use).
@@ -66,7 +66,7 @@ Generates repository documentation from the knowledge graph using an LLM. Requir
 ### list — Show all indexed repos
 
 ```bash
-npx gitnexus list
+gitnexus list
 ```
 
 Lists all repositories registered in `~/.gitnexus/registry.json`. The MCP `list_repos` tool provides the same information.

gitnexus/skills/gitnexus-debugging.md

@@ -22,7 +22,7 @@ description: "Use when the user is debugging a bug, tracing an error, or asking
 4. gitnexus_cypher({query: "MATCH path..."})                 → Custom traces if needed
 ```
 
-> If "Index is stale" → run `npx gitnexus analyze` in terminal.
+> If "Index is stale" → run `gitnexus analyze` in terminal (or `npx gitnexus analyze` if the CLI is not installed).
 
 ## Checklist
 

gitnexus/skills/gitnexus-exploring.md

@@ -23,7 +23,7 @@ description: "Use when the user asks how code works, wants to understand archite
 5. READ gitnexus://repo/{name}/process/{name}      → Trace full execution flow
 ```
 
-> If step 2 says "Index is stale" → run `npx gitnexus analyze` in terminal.
+> If step 2 says "Index is stale" → run `gitnexus analyze` in terminal (or `npx gitnexus analyze` if the CLI is not installed).
 
 ## Checklist
 

gitnexus/skills/gitnexus-guide.md

@@ -15,7 +15,7 @@ For any task involving code understanding, debugging, impact analysis, or refact
 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.
+> If step 1 warns the index is stale, run `gitnexus analyze` in the terminal first (or `npx gitnexus analyze` if the CLI is not installed).
 
 ## Skills
 

gitnexus/skills/gitnexus-impact-analysis.md

@@ -23,7 +23,7 @@ description: "Use when the user wants to know what will break if they change som
 4. Assess risk and report to user
 ```
 
-> If "Index is stale" → run `npx gitnexus analyze` in terminal.
+> If "Index is stale" → run `gitnexus analyze` in terminal (or `npx gitnexus analyze` if the CLI is not installed).
 
 ## Checklist
 

gitnexus/skills/gitnexus-pr-review.md

@@ -26,7 +26,7 @@ description: "Use when the user wants to review a pull request, understand what
 6. Summarize findings with risk assessment
 ```
 
-> If "Index is stale" → run `npx gitnexus analyze` in terminal before reviewing.
+> If "Index is stale" → run `gitnexus analyze` in terminal before reviewing (or `npx gitnexus analyze` if the CLI is not installed).
 
 ## Checklist
 

gitnexus/skills/gitnexus-refactoring.md

@@ -22,7 +22,7 @@ description: "Use when the user wants to rename, extract, split, move, or restru
 4. Plan update order: interfaces → implementations → callers → tests
 ```
 
-> If "Index is stale" → run `npx gitnexus analyze` in terminal.
+> If "Index is stale" → run `gitnexus analyze` in terminal (or `npx gitnexus analyze` if the CLI is not installed).
 
 ## Checklists