feat: smart subtree-aware reinit and validate --fix

- project_map_reinit now regenerates only the target subtree + ancestors
  by default, falling back to full reinit when subtree file count exceeds
  reinitFullThresholdPercent (default 10%).
- Add reinitFullThresholdPercent config option.
- Expose fix=true on project_map_validate Pi tool for localized repair.
- Update docs and runtime guidance to prefer patch / validate --fix
  before full reinit.
- Add integration tests for smart reinit and update typebox mock.

SKILL.md

@@ -44,8 +44,10 @@ When project-map artifacts exist in the repo:
 3. read the local `.pi-map.md` plus relevant source before editing
 4. run `project_map_patch <file>` (tool) or `project-map patch <file>` (CLI) after each source edit
 5. run `project_map_validate` (tool) or `project-map validate` (CLI) before freshness-sensitive architectural decisions or final handoff
-6. for targeted exploration, use `project_map_context <query>` (tool) or `project-map context <query>` (CLI)
-7. in `strict` mode, only bypass the protocol-path guard with an explicit marker: `[PI_MAP_BYPASS: <brief justification>]`
+6. if validation shows localized discrepancies, run `project_map_validate` with `fix=true` (tool) or `project-map validate --fix` (CLI)
+7. only if discrepancies are widespread or structural, run `project_map_reinit` (tool) or `project-map reinit` (CLI)
+8. for targeted exploration, use `project_map_context <query>` (tool) or `project-map context <query>` (CLI)
+9. in `strict` mode, only bypass the protocol-path guard with an explicit marker: `[PI_MAP_BYPASS: <brief justification>]`
 
 ## Prompt injection modes
 
@@ -102,12 +104,15 @@ Create `.pi-project-map.json` in the project root:
   "workflowHintCap": 5,
   "llmProvider": "openai",
   "llmModel": "gpt-4o-mini",
+  "reinitFullThresholdPercent": 10,
   "ignorePatterns": ["node_modules", ".git", "dist", "build"]
 }
 ```
 
 Providing `ignorePatterns` replaces the built-in default list, so include any defaults you want to keep.
 
+- `reinitFullThresholdPercent` — when `project_map_reinit` targets a subtree that covers more than this percentage of project files, it falls back to full regeneration
+
 Knobs that matter in practice:
 - `promptInjectionMode` — `off` | `advisory` | `strong` | `strict`
 - `contextBudgetPercent` / `contextBudgetMaxTokens` — caps automatic map/index injection
@@ -122,5 +127,5 @@ Knobs that matter in practice:
 | `project_map_init` | `project-map init [path]` | Generate all paired artifacts. |
 | `project_map_patch` | `project-map patch <file>` | Regenerate the pair for the changed file's directory and refresh ancestors. |
 | `project_map_validate` | `project-map validate [--fix]` | Check paired artifacts for staleness and discrepancies; optionally repair. |
-| `project_map_reinit` | `project-map reinit [path]` | Force full regeneration. |
+| `project_map_reinit` | `project-map reinit [path]` | Smart regeneration: recomputes the target subtree plus ancestors, and only falls back to full regeneration when the subtree covers more than `reinitFullThresholdPercent` of project files (default 10%). |
 | `project_map_context` | `project-map context <query>` | Retrieve a ranked context bundle for a natural-language query. |