kiri-mcp-server 0.9.6 → 0.9.9

package/dist/src/indexer/watch.js

@@ -1,7 +1,9 @@
-import { resolve } from "node:path";
+import { realpathSync, mkdirSync } from "node:fs";
+import { resolve, relative, sep, dirname, isAbsolute } from "node:path";
 import { performance } from "node:perf_hooks";
 import { watch } from "chokidar";
 import { acquireLock, releaseLock, getLockOwner, LockfileError } from "../shared/utils/lockfile.js";
+import { normalizeDbPath, normalizeRepoPath } from "../shared/utils/path.js";
 import { runIndexer } from "./cli.js";
 import { createDenylistFilter } from "./pipeline/filters/denylist.js";
 /**
@@ -21,6 +23,7 @@ import { createDenylistFilter } from "./pipeline/filters/denylist.js";
  */
 export class IndexWatcher {
     options;
+    rawRepoRoot;
     watcher = null;
     reindexTimer = null;
     isReindexing = false;
@@ -29,11 +32,28 @@ export class IndexWatcher {
     pendingFiles = new Set();
     stats;
     lockfilePath;
+    realpathCache = new Map();
     isStopping = false; // Flag to prevent new reindexes during shutdown
     constructor(options) {
+        this.rawRepoRoot = resolve(options.repoRoot);
+        const repoRoot = normalizeRepoPath(this.rawRepoRoot);
+        let databasePath;
+        // Fix #2: Ensure parent directory exists BEFORE normalization
+        // This guarantees consistent path normalization on first and subsequent runs
+        // Using sync version because constructors can't be async
+        try {
+            const parentDir = dirname(resolve(options.databasePath));
+            mkdirSync(parentDir, { recursive: true });
+        }
+        catch {
+            // Ignore if already exists or permission denied
+        }
+        // Critical: Use normalizeDbPath to ensure consistent path with cli.ts
+        // This prevents lock file and queue key mismatch
+        databasePath = normalizeDbPath(options.databasePath);
         this.options = {
-            repoRoot: resolve(options.repoRoot),
-            databasePath: resolve(options.databasePath),
+            repoRoot,
+            databasePath,
             debounceMs: options.debounceMs ?? 500,
         };
         if (options.configPath) {
@@ -57,6 +77,72 @@ export class IndexWatcher {
             });
         }
     }
+    getCachedRealPath(absPath) {
+        const cached = this.realpathCache.get(absPath);
+        if (cached) {
+            return cached;
+        }
+        try {
+            const realPath = realpathSync.native(absPath);
+            this.realpathCache.set(absPath, realPath);
+            if (this.realpathCache.size > 2048) {
+                const key = this.realpathCache.keys().next().value;
+                if (key) {
+                    this.realpathCache.delete(key);
+                }
+            }
+            return realPath;
+        }
+        catch {
+            return null;
+        }
+    }
+    /**
+     * Normalizes absolute file path to repository-relative path.
+     *
+     * Fix #3: Proper cross-platform path handling to prevent denylist bypass on Windows.
+     *
+     * Strategy:
+     * - Use path.relative() instead of string replacement
+     * - Normalize path separator to forward slash (git-compatible)
+     * - Reject paths outside repository (security check)
+     * - Reject Windows cross-drive paths and UNC paths
+     * - Resolve symlinks to prevent bypass via junctions/symlinks
+     *
+     * @param absPath - Absolute path from file watcher
+     * @returns Git-compatible relative path, or null if outside repo
+     */
+    normalizePathForRepo(absPath) {
+        const rel = relative(this.options.repoRoot, absPath);
+        // Fix #3: Security - Reject paths outside repository
+        // - Parent directory traversal: ".."
+        // - Absolute paths (Unix): starts with "/"
+        // - Absolute paths (Windows): starts with drive letter "C:" or "C:\"
+        // - UNC paths (Windows): starts with "\\" or "//"
+        // Note: Empty string is ALLOWED (represents repo root for chokidar directory watching)
+        if (rel.startsWith("..") ||
+            isAbsolute(rel) ||
+            /^[A-Za-z]:/.test(rel) ||
+            rel.startsWith("\\\\") ||
+            rel.startsWith("//")) {
+            return null;
+        }
+        // Fix #3: Additional safety - Resolve symlinks once and cache the result
+        // This prevents bypass via junction points or symlinks pointing outside the repo
+        const realAbsPath = this.getCachedRealPath(absPath);
+        if (realAbsPath) {
+            const realRepoRoot = this.options.repoRoot; // Already normalized in constructor
+            const realRel = relative(realRepoRoot, realAbsPath);
+            // Double-check the real path is still inside repo
+            if (realRel.startsWith("..") || isAbsolute(realRel)) {
+                return null;
+            }
+        }
+        // Allow empty string (repo root itself) for chokidar directory watching
+        // Normalize to forward slash for cross-platform compatibility
+        // Windows uses backslash, but git and denylist rules expect forward slash
+        return rel.split(sep).join("/");
+    }
     /**
      * Starts the file watcher and begins monitoring for changes.
      *
@@ -73,7 +159,11 @@ export class IndexWatcher {
             persistent: true,
             ignoreInitial: true, // Don't trigger on existing files
             ignored: (path) => {
-                const relativePath = path.replace(this.options.repoRoot + "/", "");
+                const relativePath = this.normalizePathForRepo(path);
+                // Reject paths outside repo or invalid paths (explicit null check, not falsy check)
+                if (relativePath === null) {
+                    return true;
+                }
                 return denylistFilter.isDenied(relativePath);
             },
             // Editor-specific handling
@@ -85,17 +175,47 @@ export class IndexWatcher {
             usePolling: false, // Use native OS events (faster)
             // depth option omitted for no depth limit
         });
-        // Register event handlers
-        this.watcher
-            .on("add", (path) => this.scheduleReindex("add", path))
-            .on("change", (path) => this.scheduleReindex("change", path))
-            .on("unlink", (path) => this.scheduleReindex("unlink", path))
-            .on("error", (error) => {
-            process.stderr.write(`❌ File watcher error: ${error instanceof Error ? error.message : String(error)}\n`);
-        })
-            .on("ready", () => {
-            process.stderr.write(`👁️  Watch mode started. Monitoring ${this.options.repoRoot} for changes...\n`);
-            process.stderr.write(`   Debounce: ${this.options.debounceMs}ms\n`);
+        // Return promise that resolves when watcher is fully initialized
+        return new Promise((resolve, reject) => {
+            const watcher = this.watcher;
+            let settled = false;
+            const settle = (cb) => {
+                if (settled) {
+                    return;
+                }
+                settled = true;
+                cb();
+            };
+            const handleError = (error) => {
+                process.stderr.write(`❌ File watcher error: ${error instanceof Error ? error.message : String(error)}\n`);
+                if (this.watcher) {
+                    void this.watcher.close().catch(() => {
+                        /* ignore */
+                    });
+                    this.watcher = null;
+                }
+                settle(() => {
+                    reject(new Error(`Failed to start watch mode: ${error instanceof Error ? error.message : String(error)}`));
+                });
+            };
+            // Register event handlers
+            watcher
+                .on("add", (path) => {
+                this.scheduleReindex("add", path);
+            })
+                .on("change", (path) => {
+                this.scheduleReindex("change", path);
+            })
+                .on("unlink", (path) => {
+                this.scheduleReindex("unlink", path);
+            })
+                .on("error", handleError)
+                .once("ready", () => {
+                watcher.off("error", handleError);
+                process.stderr.write(`👁️  Watch mode started. Monitoring ${this.options.repoRoot} for changes...\n`);
+                process.stderr.write(`   Debounce: ${this.options.debounceMs}ms\n`);
+                settle(resolve);
+            });
         });
     }
     /**
@@ -111,7 +231,11 @@ export class IndexWatcher {
         if (this.isStopping) {
             return;
         }
-        const relativePath = path.replace(this.options.repoRoot + "/", "");
+        const relativePath = this.normalizePathForRepo(path);
+        // Ignore paths outside repository (security check)
+        if (!relativePath) {
+            return;
+        }
         this.pendingFiles.add(relativePath);
         // Clear existing timer if present
         if (this.reindexTimer !== null) {
@@ -126,9 +250,11 @@ export class IndexWatcher {
             const moreCount = Math.max(0, this.pendingFiles.size - 5);
             const summary = moreCount > 0 ? `${fileList} (+${moreCount} more)` : fileList;
             process.stderr.write(`\n📝 File changes detected: ${summary}\n`);
-            // Clear pending files and trigger reindex
+            // Fix #3 & #4: Capture snapshot BEFORE clearing to prevent data loss and enable incremental indexing
+            const changedPaths = Array.from(this.pendingFiles);
             this.pendingFiles.clear();
-            void this.executeReindex();
+            // Pass snapshot to executeReindex
+            void this.executeReindex(changedPaths);
         }, this.options.debounceMs);
         // Mark pending flag (used if reindex is already running)
         this.pendingReindex = true;
@@ -138,8 +264,10 @@ export class IndexWatcher {
      *
      * If a reindex is already in progress, marks a pending flag to trigger
      * another reindex after the current one completes.
+     *
+     * @param changedPaths - Array of file paths that changed (Fix #3 & #4: snapshot from scheduleReindex)
      */
-    async executeReindex() {
+    async executeReindex(changedPaths) {
         // Don't start reindex if watcher is stopping
         if (this.isStopping) {
             process.stderr.write(`🛑 Watcher stopping. Skipping reindex.\n`);
@@ -147,6 +275,10 @@ export class IndexWatcher {
         }
         // Check if already reindexing
         if (this.isReindexing) {
+            // Fix #6: Restore changedPaths back to pendingFiles to prevent data loss
+            for (const path of changedPaths) {
+                this.pendingFiles.add(path);
+            }
             process.stderr.write(`⏳ Reindex already in progress. Will reindex again after completion.\n`);
             this.pendingReindex = true;
             return;
@@ -154,10 +286,12 @@ export class IndexWatcher {
         this.isReindexing = true;
         this.pendingReindex = false;
         this.stats.lastReindexStart = performance.now();
-        // Capture pending files for incremental indexing
-        const changedPaths = Array.from(this.pendingFiles);
+        // Fix #3 & #4: Use changedPaths parameter (snapshot from scheduleReindex) instead of reading pendingFiles
+        // This prevents data loss on lock contention and enables true incremental indexing
         // Create and store the reindex promise for proper shutdown handling
         this.reindexPromise = (async () => {
+            // Fix #1: Track lock ownership to prevent releasing locks we don't own
+            let lockAcquired = false;
             try {
                 // Double-check stopping flag before acquiring lock
                 if (this.isStopping) {
@@ -167,12 +301,18 @@ export class IndexWatcher {
                 // Acquire lock to prevent concurrent indexing
                 try {
                     acquireLock(this.lockfilePath);
+                    lockAcquired = true; // Fix #1: Only set to true on successful acquisition
                 }
                 catch (error) {
                     if (error instanceof LockfileError) {
+                        // Fix #3: Restore changedPaths to pendingFiles to prevent data loss
+                        for (const path of changedPaths) {
+                            this.pendingFiles.add(path);
+                        }
+                        this.pendingReindex = true; // Mark for retry when lock is available
                         const ownerPid = error.ownerPid ?? getLockOwner(this.lockfilePath);
                         const ownerInfo = ownerPid ? ` (PID: ${ownerPid})` : "";
-                        process.stderr.write(`⚠️  Another indexing process${ownerInfo} holds the lock. Skipping this reindex.\n`);
+                        process.stderr.write(`⚠️  Another indexing process${ownerInfo} holds the lock. Changes queued for retry.\n`);
                         return;
                     }
                     throw error;
@@ -181,10 +321,11 @@ export class IndexWatcher {
                 const start = performance.now();
                 process.stderr.write(`🔄 Incrementally reindexing ${changedPaths.length} file(s)...\n`);
                 await runIndexer({
-                    repoRoot: this.options.repoRoot,
+                    repoRoot: this.rawRepoRoot,
                     databasePath: this.options.databasePath,
                     full: false,
                     changedPaths,
+                    skipLocking: true, // Fix #1: Watcher already holds the lock
                 });
                 const duration = performance.now() - start;
                 this.stats.reindexCount++;
@@ -198,22 +339,42 @@ export class IndexWatcher {
                 }
             }
             catch (error) {
+                // Fix #2: Restore changedPaths for ALL errors, not just LockfileError
+                // This prevents permanent data loss when reindex fails due to:
+                // - Database I/O errors
+                // - Parsing failures
+                // - Network timeouts
+                // - Any other transient errors
+                for (const path of changedPaths) {
+                    this.pendingFiles.add(path);
+                }
+                this.pendingReindex = true;
                 process.stderr.write(`❌ Reindex failed: ${error instanceof Error ? error.message : String(error)}\n`);
-                process.stderr.write(`   Watch mode continues. Next change will trigger reindex.\n`);
+                process.stderr.write(`   Changes queued for retry on next file event.\n`);
             }
             finally {
                 this.isReindexing = false;
-                releaseLock(this.lockfilePath);
+                // Fix #1: Only release lock if we acquired it (prevents deleting other process's locks)
+                if (lockAcquired) {
+                    releaseLock(this.lockfilePath);
+                }
                 this.reindexPromise = null;
                 // Clear timer to prevent resource leak
                 if (this.reindexTimer !== null) {
                     clearTimeout(this.reindexTimer);
                     this.reindexTimer = null;
                 }
-                // If more changes occurred during reindex, schedule another one
-                if (this.pendingReindex) {
+                // Fix #7: If more changes occurred during reindex, trigger direct retry
+                if (this.pendingReindex && this.pendingFiles.size > 0) {
                     process.stderr.write(`🔁 New changes detected during reindex. Scheduling another reindex...\n`);
-                    this.scheduleReindex("batch", "(multiple files)");
+                    // Direct retry without file system event dependency
+                    // Don't clear pendingFiles here - let the timer callback handle it
+                    this.reindexTimer = setTimeout(() => {
+                        this.reindexTimer = null;
+                        const changedPaths = Array.from(this.pendingFiles);
+                        this.pendingFiles.clear();
+                        void this.executeReindex(changedPaths);
+                    }, this.options.debounceMs);
                 }
             }
         })();

package/dist/src/indexer/watch.js.map

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package/dist/src/server/context.d.ts

@@ -1,11 +1,18 @@
 import { DuckDBClient } from "../shared/duckdb.js";
 import { WarningManager } from "./rpc.js";
+export interface FtsStatusCache {
+    ready: boolean;
+    schemaExists: boolean;
+    anyDirty: boolean;
+    lastChecked: number;
+}
 export interface ServerContext {
     db: DuckDBClient;
     repoId: number;
     features?: {
         fts?: boolean;
     };
+    ftsStatusCache?: FtsStatusCache;
     warningManager: WarningManager;
 }
 //# sourceMappingURL=context.d.ts.map

package/dist/src/server/context.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"context.d.ts","sourceRoot":"","sources":["../../../src/server/context.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,YAAY,EAAE,MAAM,qBAAqB,CAAC;AAEnD,OAAO,EAAE,cAAc,EAAE,MAAM,UAAU,CAAC;AAE1C,MAAM,WAAW,aAAa;IAC5B,EAAE,EAAE,YAAY,CAAC;IACjB,MAAM,EAAE,MAAM,CAAC;IACf,QAAQ,CAAC,EAAE;QACT,GAAG,CAAC,EAAE,OAAO,CAAC;KACf,CAAC;IACF,cAAc,EAAE,cAAc,CAAC;CAChC"}
+{"version":3,"file":"context.d.ts","sourceRoot":"","sources":["../../../src/server/context.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,YAAY,EAAE,MAAM,qBAAqB,CAAC;AAEnD,OAAO,EAAE,cAAc,EAAE,MAAM,UAAU,CAAC;AAE1C,MAAM,WAAW,cAAc;IAC7B,KAAK,EAAE,OAAO,CAAC;IACf,YAAY,EAAE,OAAO,CAAC;IACtB,QAAQ,EAAE,OAAO,CAAC;IAClB,WAAW,EAAE,MAAM,CAAC;CACrB;AAED,MAAM,WAAW,aAAa;IAC5B,EAAE,EAAE,YAAY,CAAC;IACjB,MAAM,EAAE,MAAM,CAAC;IACf,QAAQ,CAAC,EAAE;QACT,GAAG,CAAC,EAAE,OAAO,CAAC;KACf,CAAC;IACF,cAAc,CAAC,EAAE,cAAc,CAAC;IAChC,cAAc,EAAE,cAAc,CAAC;CAChC"}

package/dist/src/server/handlers.d.ts.map

@@ -1 +1 @@
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package/dist/src/server/handlers.js

@@ -1,6 +1,8 @@
 import path from "node:path";
+import { checkFTSSchemaExists } from "../indexer/schema.js";
 import { generateEmbedding, structuralSimilarity } from "../shared/embedding.js";
 import { encode as encodeGPT, tokenizeText } from "../shared/tokenizer.js";
+import { getRepoPathCandidates, normalizeRepoPath } from "../shared/utils/path.js";
 import { coerceProfileName, loadScoringProfile } from "./scoring.js";
 // Configuration file patterns (v0.8.0+: consolidated to avoid duplication)
 // Comprehensive list covering multiple languages and tools
@@ -127,6 +129,67 @@ const CONFIG_PATTERNS = [
     ".circleci/config.yml",
     ".github/workflows",
 ];
+const FTS_STATUS_CACHE_TTL_MS = 10_000;
+async function hasDirtyRepos(db) {
+    const statusCheck = await db.all(`SELECT COUNT(*) as count FROM repo
+       WHERE fts_dirty = true OR fts_status IN ('dirty', 'rebuilding')`);
+    return (statusCheck[0]?.count ?? 0) > 0;
+}
+async function refreshFtsStatus(context) {
+    const previousReady = context.features?.fts ?? false;
+    const cache = {
+        ready: false,
+        schemaExists: false,
+        anyDirty: false,
+        lastChecked: Date.now(),
+    };
+    try {
+        cache.schemaExists = await checkFTSSchemaExists(context.db);
+        if (!cache.schemaExists) {
+            context.warningManager.warnForRequest("fts-schema-missing", "FTS schema not found, falling back to ILIKE");
+        }
+        else {
+            cache.anyDirty = await hasDirtyRepos(context.db);
+            if (cache.anyDirty) {
+                context.warningManager.warnForRequest("fts-stale", "FTS index is stale or rebuilding, using ILIKE fallback. Run indexer to update FTS.");
+            }
+            else {
+                await context.db.run("LOAD fts;");
+                cache.ready = true;
+            }
+        }
+    }
+    catch (error) {
+        cache.ready = false;
+        cache.schemaExists = false;
+        context.warningManager.warnForRequest("fts-check-failed", `FTS availability check failed: ${error}`);
+    }
+    if (!context.features) {
+        context.features = {};
+    }
+    context.features.fts = cache.ready;
+    context.ftsStatusCache = cache;
+    if (cache.ready && !previousReady) {
+        console.info("✅ FTS recovered and enabled");
+    }
+    else if (!cache.ready && previousReady) {
+        console.warn("⚠️  FTS became unavailable; falling back to ILIKE");
+    }
+    return cache;
+}
+async function getFreshFtsStatus(context) {
+    const cache = context.ftsStatusCache;
+    if (cache && Date.now() - cache.lastChecked < FTS_STATUS_CACHE_TTL_MS) {
+        if (cache.ready) {
+            const dirtyNow = await hasDirtyRepos(context.db);
+            if (dirtyNow) {
+                return refreshFtsStatus(context);
+            }
+        }
+        return cache;
+    }
+    return refreshFtsStatus(context);
+}
 /**
  * Check if a file path represents a configuration file
  * Supports multiple languages: JS/TS, Python, Ruby, Go, PHP, Java, Rust, C/C++, Docker, CI/CD
@@ -634,8 +697,14 @@ function applyFileTypeBoost(path, baseScore, profile = "default", weights) {
         ".git/",
         "node_modules/",
     ];
-    if (blacklistedDirs.some((dir) => path.startsWith(dir))) {
-        return -100; // Effectively remove it
+    for (const dir of blacklistedDirs) {
+        if (path.startsWith(dir)) {
+            // FIX: boost_profile="docs" の場合は docs/ ブラックリストをスキップ
+            if (profile === "docs" && dir === "docs/") {
+                continue;
+            }
+            return -100; // Effectively remove it
+        }
     }
     if (profile === "none") {
         return baseScore;
@@ -913,7 +982,8 @@ export async function filesSearch(context, params) {
         throw new Error("files_search requires a non-empty query. Provide a search keyword to continue.");
     }
     const limit = normalizeLimit(params.limit);
-    const hasFTS = context.features?.fts ?? false;
+    const ftsStatus = await getFreshFtsStatus(context);
+    const hasFTS = ftsStatus.ready;
     let sql;
     let values;
     if (hasFTS) {
@@ -1669,14 +1739,27 @@ export async function depsClosure(context, params) {
 }
 export async function resolveRepoId(db, repoRoot) {
     try {
-        const rows = await db.all("SELECT id FROM repo WHERE root = ?", [repoRoot]);
+        const candidates = getRepoPathCandidates(repoRoot);
+        const normalized = candidates[0];
+        const placeholders = candidates.map(() => "?").join(", ");
+        const rows = await db.all(`SELECT id, root FROM repo WHERE root IN (${placeholders}) LIMIT 1`, candidates);
         if (rows.length === 0) {
+            const existingRows = await db.all("SELECT id, root FROM repo");
+            for (const candidate of existingRows) {
+                if (normalizeRepoPath(candidate.root) === normalized) {
+                    await db.run("UPDATE repo SET root = ? WHERE id = ?", [normalized, candidate.id]);
+                    return candidate.id;
+                }
+            }
             throw new Error("Target repository is missing from DuckDB. Run the indexer before starting the server.");
         }
         const row = rows[0];
         if (!row) {
             throw new Error("Failed to retrieve repository record. Database returned empty result.");
         }
+        if (row.root !== normalized) {
+            await db.run("UPDATE repo SET root = ? WHERE id = ?", [normalized, row.id]);
+        }
         return row.id;
     }
     catch (error) {