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.

src/patch.ts

@@ -5,6 +5,7 @@ import {
 	discoverProject,
 	generateDirectoryArtifacts,
 	buildDirectoryContext,
+	getAncestorEntries,
 } from "./init.js";
 import type { DirectoryEntry } from "./discover.js";
 import type { LLMClient } from "./llm/llm-client.js";
@@ -133,25 +134,6 @@ function countDirectChildren(rootPath: string, relDir: string): number {
 	}).length;
 }
 
-function getAncestorEntries(
-	entries: DirectoryEntry[],
-	ctx: ReturnType<typeof buildDirectoryContext>,
-	entry: DirectoryEntry,
-): DirectoryEntry[] {
-	const result: DirectoryEntry[] = [];
-	let parent = ctx.parentMap.get(entry.relativePath);
-	while (parent) {
-		const ancestor = entries.find(
-			(candidate) => candidate.relativePath === parent,
-		);
-		if (ancestor) {
-			result.push(ancestor);
-		}
-		parent = ctx.parentMap.get(parent);
-	}
-	return result;
-}
-
 function normalizeRelativePath(relPath: string): string {
 	if (!relPath || relPath === ".") return ".";
 	return relPath.replace(/\\/g, "/");