ultraclaude-agent 0.0.16 → 0.0.17

package/dist/sync.d.ts

@@ -36,6 +36,11 @@ export declare function createProjectOnServer(name: string, slug: string, creden
     id: string;
 } | null>;
 export declare function createSnapshot(projectId: string, name: string, commitHash?: string, trigger?: string, credentials?: AgentCredentials): Promise<boolean>;
+/**
+ * Notify the server that specific files have been deleted from disk.
+ * Cleans up synced_files, document_sections, plans, and backlog entries.
+ */
+export declare function deleteFiles(projectId: string, projectPath: string, absoluteFilePaths: string[], credentials: AgentCredentials): Promise<boolean>;
 export declare function initialSync(projectId: string, projectPath: string, credentials: AgentCredentials): Promise<void>;
 export declare function getQueueSize(): number;
 export declare function stopSync(): void;

package/dist/sync.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"sync.d.ts","sourceRoot":"","sources":["../src/sync.ts"],"names":[],"mappings":"AAIA,OAAO,EAKL,KAAK,gBAAgB,EAErB,KAAK,aAAa,EAClB,KAAK,MAAM,EACZ,MAAM,sBAAsB,CAAC;AA4C9B,KAAK,eAAe,GAAG,eAAe,GAAG,eAAe,CAAC;AAEzD;;;GAGG;AACH,wBAAsB,UAAU,CAC9B,MAAM,EAAE,MAAM,EACd,IAAI,EAAE,MAAM,EACZ,IAAI,EAAE,OAAO,GAAG,SAAS,EACzB,WAAW,EAAE,gBAAgB,EAC7B,YAAY,CAAC,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,GACpC,OAAO,CAAC,MAAM,CAAC,QAAQ,EAAE,eAAe,CAAC,CAAC,CAgB5C;AAED;;;;GAIG;AACH,wBAAsB,6BAA6B,CACjD,MAAM,EAAE,MAAM,EACd,IAAI,EAAE,MAAM,EACZ,IAAI,CAAC,EAAE,OAAO,EACd,YAAY,CAAC,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,GACpC,OAAO,CAAC,MAAM,CAAC,QAAQ,EAAE,eAAe,CAAC,CAAC,CAI5C;AAID,KAAK,aAAa,GAAG,eAAe,GAAG,eAAe,GAAG,uBAAuB,GAAG,mBAAmB,CAAC;AAEvG,wBAAsB,aAAa,CAAC,SAAS,EAAE,MAAM,EAAE,WAAW,EAAE,gBAAgB,GAAG,OAAO,CAAC,MAAM,CAAC,aAAa,EAAE,EAAE,aAAa,CAAC,CAAC,CA8BrI;AAED;;GAEG;AACH,wBAAsB,qBAAqB,CAAC,SAAS,EAAE,MAAM,EAAE,WAAW,EAAE,gBAAgB,GAAG,OAAO,CAAC,IAAI,CAAC,CAgB3G;AAID;;;GAGG;AACH,wBAAsB,gBAAgB,CACpC,SAAS,EAAE,MAAM,EACjB,WAAW,EAAE,MAAM,EACnB,gBAAgB,EAAE,MAAM,EACxB,WAAW,EAAE,gBAAgB,GAC5B,OAAO,CAAC,MAAM,CAAC,CAyFjB;AAID,wBAAsB,YAAY,CAChC,SAAS,EAAE,MAAM,EACjB,WAAW,EAAE,MAAM,EACnB,gBAAgB,EAAE,MAAM,EACxB,WAAW,EAAE,gBAAgB,GAC5B,OAAO,CAAC,OAAO,CAAC,CAgDlB;AAID,wBAAsB,QAAQ,CAC5B,SAAS,EAAE,MAAM,EACjB,WAAW,EAAE,MAAM,EACnB,gBAAgB,EAAE,MAAM,EACxB,WAAW,EAAE,gBAAgB,GAC5B,OAAO,CAAC,IAAI,CAAC,CAMf;AAID;;;GAGG;AACH,wBAAsB,mBAAmB,CACvC,SAAS,EAAE,MAAM,EACjB,WAAW,EAAE,MAAM,EACnB,WAAW,EAAE,gBAAgB,GAC5B,OAAO,CAAC,IAAI,CAAC,CA+Bf;AAID,wBAAsB,qBAAqB,CACzC,IAAI,EAAE,MAAM,EACZ,IAAI,EAAE,MAAM,EACZ,WAAW,EAAE,gBAAgB,EAC7B,WAAW,CAAC,EAAE;IAAE,YAAY,CAAC,EAAE,MAAM,CAAC;IAAC,eAAe,CAAC,EAAE,MAAM,CAAA;CAAE,GAChE,OAAO,CAAC;IAAE,EAAE,EAAE,MAAM,CAAA;CAAE,GAAG,IAAI,CAAC,CAyBhC;AAID,wBAAsB,cAAc,CAClC,SAAS,EAAE,MAAM,EACjB,IAAI,EAAE,MAAM,EACZ,UAAU,CAAC,EAAE,MAAM,EACnB,OAAO,GAAE,MAAiB,EAC1B,WAAW,CAAC,EAAE,gBAAgB,GAC7B,OAAO,CAAC,OAAO,CAAC,CAyBlB;AAID;;;GAGG;AACH,wBAAsB,WAAW,CAC/B,SAAS,EAAE,MAAM,EACjB,WAAW,EAAE,MAAM,EACnB,iBAAiB,EAAE,MAAM,EAAE,EAC3B,WAAW,EAAE,gBAAgB,GAC5B,OAAO,CAAC,OAAO,CAAC,CAiClB;AA0CD,wBAAsB,WAAW,CAC/B,SAAS,EAAE,MAAM,EACjB,WAAW,EAAE,MAAM,EACnB,WAAW,EAAE,gBAAgB,GAC5B,OAAO,CAAC,IAAI,CAAC,CA8Bf;AAgFD,wBAAgB,YAAY,IAAI,MAAM,CAErC;AAED,wBAAgB,QAAQ,IAAI,IAAI,CAI/B"}

package/dist/sync.js

@@ -306,14 +306,74 @@ export async function createSnapshot(projectId, name, commitHash, trigger = 'man
     log.info({ name }, 'Snapshot created');
     return true;
 }
+// --- Delete files ---
+/**
+ * Notify the server that specific files have been deleted from disk.
+ * Cleans up synced_files, document_sections, plans, and backlog entries.
+ */
+export async function deleteFiles(projectId, projectPath, absoluteFilePaths, credentials) {
+    const log = logger.child({ projectId, op: 'deleteFiles' });
+    const docDir = join(projectPath, 'documentation');
+    const relativePaths = absoluteFilePaths.map((p) => relative(docDir, p));
+    const payload = { projectId, files: relativePaths };
+    const idempotencyKey = crypto.randomUUID();
+    const result = await apiRequest('POST', '/api/sync/delete-files', payload, credentials, {
+        'Idempotency-Key': idempotencyKey,
+    });
+    if (!result.success || !result.data.ok) {
+        const reason = !result.success ? result.message : `HTTP ${result.data.status}`;
+        log.warn({ error: reason, files: relativePaths }, 'Delete-files request failed');
+        return false;
+    }
+    // Clear local cache entries for deleted files
+    const state = getOrCreateState(projectId);
+    for (const relPath of relativePaths) {
+        state.fileHashes.delete(relPath);
+        // Clear section hashes for this file
+        for (const key of state.sectionHashes.keys()) {
+            if (key.startsWith(`${relPath}#`)) {
+                state.sectionHashes.delete(key);
+            }
+        }
+    }
+    log.info({ count: relativePaths.length }, 'Files deleted on server');
+    return true;
+}
+// --- Reconcile ---
+/**
+ * Tell the server the full set of files currently on disk.
+ * Server prunes synced_files, plans, and backlog items not in this set.
+ */
+async function reconcile(projectId, activePaths, credentials) {
+    const log = logger.child({ projectId, op: 'reconcile' });
+    const payload = { projectId, filePaths: activePaths };
+    const idempotencyKey = crypto.randomUUID();
+    const result = await apiRequest('POST', '/api/sync/reconcile', payload, credentials, {
+        'Idempotency-Key': idempotencyKey,
+    });
+    if (!result.success || !result.data.ok) {
+        const reason = !result.success ? result.message : `HTTP ${result.data.status}`;
+        log.warn({ error: reason }, 'Reconcile request failed — orphaned data may persist until next sync');
+        return;
+    }
+    const body = (await result.data.json());
+    const { prunedFiles, prunedPlans, prunedBacklogItems } = body.data;
+    if (prunedFiles > 0 || prunedPlans > 0 || prunedBacklogItems > 0) {
+        log.info({ prunedFiles, prunedPlans, prunedBacklogItems }, 'Reconciliation pruned orphaned data');
+    }
+    else {
+        log.debug('Reconciliation complete — no orphans found');
+    }
+}
 // --- Initial sync for a project ---
 export async function initialSync(projectId, projectPath, credentials) {
     const log = logger.child({ projectId, op: 'initialSync' });
     log.info('Starting initial sync');
     await loadManifestIntoCache(projectId, credentials);
-    // Walk documentation/ and sync all files
+    // Walk documentation/ and sync all files, collecting relative paths
     const { glob } = await import('node:fs/promises');
     const docDir = join(projectPath, 'documentation');
+    const activePaths = [];
     try {
         for await (const entry of glob(join(docDir, '**/*'), {})) {
             const fileStat = await stat(entry).catch(() => null);
@@ -321,8 +381,12 @@ export async function initialSync(projectId, projectPath, credentials) {
                 continue;
             if (fileStat.size > MAX_FILE_SIZE)
                 continue;
+            const relPath = relative(docDir, entry);
+            activePaths.push(relPath);
             await syncFile(projectId, projectPath, entry, credentials);
         }
+        // Reconcile: prune server-side data for files that no longer exist on disk
+        await reconcile(projectId, activePaths, credentials);
         log.info('Initial sync complete');
     }
     catch (err) {

package/dist/sync.js.map

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package/dist/watcher.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"watcher.d.ts","sourceRoot":"","sources":["../src/watcher.ts"],"names":[],"mappings":"AAOA,OAAO,KAAK,EAAE,gBAAgB,EAAE,MAAM,sBAAsB,CAAC;AAE7D,UAAU,qBAAqB;IAC7B,SAAS,EAAE,MAAM,CAAC;IAClB,WAAW,EAAE,MAAM,CAAC;IACpB,WAAW,EAAE,gBAAgB,CAAC;CAC/B;AAED,MAAM,WAAW,cAAc;IAC7B,SAAS,EAAE,MAAM,CAAC;IAClB,WAAW,EAAE,MAAM,CAAC;IACpB,WAAW,EAAE,gBAAgB,CAAC;IAC9B,KAAK,IAAI,OAAO,CAAC,IAAI,CAAC,CAAC;CACxB;AAED;;;;;GAKG;AACH,wBAAgB,mBAAmB,CAAC,OAAO,EAAE,qBAAqB,GAAG,cAAc,CAqHlF"}
+{"version":3,"file":"watcher.d.ts","sourceRoot":"","sources":["../src/watcher.ts"],"names":[],"mappings":"AAOA,OAAO,KAAK,EAAE,gBAAgB,EAAE,MAAM,sBAAsB,CAAC;AAE7D,UAAU,qBAAqB;IAC7B,SAAS,EAAE,MAAM,CAAC;IAClB,WAAW,EAAE,MAAM,CAAC;IACpB,WAAW,EAAE,gBAAgB,CAAC;CAC/B;AAED,MAAM,WAAW,cAAc;IAC7B,SAAS,EAAE,MAAM,CAAC;IAClB,WAAW,EAAE,MAAM,CAAC;IACpB,WAAW,EAAE,gBAAgB,CAAC;IAC9B,KAAK,IAAI,OAAO,CAAC,IAAI,CAAC,CAAC;CACxB;AAED;;;;;GAKG;AACH,wBAAgB,mBAAmB,CAAC,OAAO,EAAE,qBAAqB,GAAG,cAAc,CA0HlF"}

package/dist/watcher.js

@@ -2,7 +2,7 @@
 // Watches documentation/ for changes, triggers section-level sync
 import chokidar from 'chokidar';
 import { join, basename } from 'node:path';
-import { syncFile, initialSync, createSnapshot, pushVersionMetadata } from './sync.js';
+import { syncFile, deleteFiles, initialSync, createSnapshot, pushVersionMetadata } from './sync.js';
 import { logger } from './logger.js';
 /**
  * Start watching a project's documentation/ directory for changes.
@@ -53,7 +53,12 @@ export function startProjectWatcher(options) {
         .on('add', handleChange)
         .on('change', handleChange)
         .on('unlink', (filePath) => {
-        log.info({ file: filePath }, 'File deleted — sections will be marked as removed on next sync');
+        log.info({ file: filePath }, 'File deleted — notifying server');
+        credentialsPromise
+            .then(creds => deleteFiles(projectId, projectPath, [filePath], creds))
+            .catch((deleteErr) => {
+            log.error({ err: deleteErr, file: filePath }, 'Delete notification failed for file');
+        });
     })
         .on('error', (err) => log.error({ err }, 'Documentation watcher error'))
         .on('ready', () => log.info('Documentation watcher ready'));

package/dist/watcher.js.map

@@ -1 +1 @@
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package/node_modules/@ultra-claude/shared/dist/api/schemas/sync.d.ts

@@ -50,4 +50,14 @@ export declare const createSnapshotSchema: z.ZodObject<{
     }>>;
 }, z.core.$strip>;
 export type CreateSnapshotInput = z.infer<typeof createSnapshotSchema>;
+export declare const deleteFilesSchema: z.ZodObject<{
+    projectId: z.ZodString;
+    files: z.ZodArray<z.ZodString>;
+}, z.core.$strip>;
+export type DeleteFilesInput = z.infer<typeof deleteFilesSchema>;
+export declare const reconcileSchema: z.ZodObject<{
+    projectId: z.ZodString;
+    filePaths: z.ZodArray<z.ZodString>;
+}, z.core.$strip>;
+export type ReconcileInput = z.infer<typeof reconcileSchema>;
 //# sourceMappingURL=sync.d.ts.map

package/node_modules/@ultra-claude/shared/dist/api/schemas/sync.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"sync.d.ts","sourceRoot":"","sources":["../../../src/api/schemas/sync.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,CAAC,EAAE,MAAM,KAAK,CAAC;AAaxB,eAAO,MAAM,iBAAiB;;;;;;;iBAO5B,CAAC;AAEH,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;iBAM7B,CAAC;AAEH,MAAM,MAAM,iBAAiB,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,kBAAkB,CAAC,CAAC;AACnE,MAAM,MAAM,WAAW,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,iBAAiB,CAAC,CAAC;AAI5D,eAAO,MAAM,kBAAkB;;;;;iBAK7B,CAAC;AAEH,eAAO,MAAM,eAAe;;;;;;;;iBAG1B,CAAC;AAEH,MAAM,MAAM,cAAc,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,eAAe,CAAC,CAAC;AAI7D,eAAO,MAAM,oBAAoB;;;;;;;;;iBAK/B,CAAC;AAEH,MAAM,MAAM,mBAAmB,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,oBAAoB,CAAC,CAAC"}
+{"version":3,"file":"sync.d.ts","sourceRoot":"","sources":["../../../src/api/schemas/sync.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,CAAC,EAAE,MAAM,KAAK,CAAC;AAaxB,eAAO,MAAM,iBAAiB;;;;;;;iBAO5B,CAAC;AAEH,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;iBAM7B,CAAC;AAEH,MAAM,MAAM,iBAAiB,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,kBAAkB,CAAC,CAAC;AACnE,MAAM,MAAM,WAAW,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,iBAAiB,CAAC,CAAC;AAI5D,eAAO,MAAM,kBAAkB;;;;;iBAK7B,CAAC;AAEH,eAAO,MAAM,eAAe;;;;;;;;iBAG1B,CAAC;AAEH,MAAM,MAAM,cAAc,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,eAAe,CAAC,CAAC;AAI7D,eAAO,MAAM,oBAAoB;;;;;;;;;iBAK/B,CAAC;AAEH,MAAM,MAAM,mBAAmB,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,oBAAoB,CAAC,CAAC;AAIvE,eAAO,MAAM,iBAAiB;;;iBAG5B,CAAC;AAEH,MAAM,MAAM,gBAAgB,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,iBAAiB,CAAC,CAAC;AAIjE,eAAO,MAAM,eAAe;;;iBAG1B,CAAC;AAEH,MAAM,MAAM,cAAc,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,eAAe,CAAC,CAAC"}

package/node_modules/@ultra-claude/shared/dist/api/schemas/sync.js

@@ -40,4 +40,14 @@ export const createSnapshotSchema = z.object({
     commitHash: z.string().max(64).optional(),
     trigger: z.enum(['manual', 'git_commit', 'plan_completion']).optional(),
 });
+// --- POST /api/sync/delete-files ---
+export const deleteFilesSchema = z.object({
+    projectId: z.string().uuid(),
+    files: z.array(safePath).min(1).max(500),
+});
+// --- POST /api/sync/reconcile ---
+export const reconcileSchema = z.object({
+    projectId: z.string().uuid(),
+    filePaths: z.array(safePath).max(10_000),
+});
 //# sourceMappingURL=sync.js.map

package/node_modules/@ultra-claude/shared/dist/api/schemas/sync.js.map

@@ -1 +1 @@
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+{"version":3,"file":"sync.js","sourceRoot":"","sources":["../../../src/api/schemas/sync.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,CAAC,EAAE,MAAM,KAAK,CAAC;AAExB,MAAM,cAAc,GAAG,uBAAuB,CAAC;AAE/C,MAAM,QAAQ,GAAG,CAAC;KACf,MAAM,EAAE;KACR,GAAG,CAAC,CAAC,CAAC;KACN,GAAG,CAAC,GAAG,CAAC;KACR,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,IAAI,CAAC,EAAE,4BAA4B,CAAC;KAC9D,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE,4BAA4B,CAAC,CAAC;AAEnE,kCAAkC;AAElC,MAAM,CAAC,MAAM,iBAAiB,GAAG,CAAC,CAAC,MAAM,CAAC;IACxC,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,GAAG,CAAC;IAChC,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC,QAAQ,EAAE;IACvC,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,QAAQ,EAAE;IAChD,QAAQ,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,CAAC,WAAW,EAAE;IACxC,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,SAAS,CAAC;IAClC,YAAY,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,KAAK,CAAC,cAAc,EAAE,4BAA4B,CAAC;CAC7E,CAAC,CAAC;AAEH,MAAM,CAAC,MAAM,kBAAkB,GAAG,CAAC,CAAC,MAAM,CAAC;IACzC,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,IAAI,EAAE;IAC5B,IAAI,EAAE,QAAQ;IACd,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,KAAK,CAAC,cAAc,EAAE,4BAA4B,CAAC;IACzE,QAAQ,EAAE,CAAC,CAAC,KAAK,CAAC,iBAAiB,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,GAAG,CAAC;IACpD,YAAY,EAAE,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC,QAAQ,EAAE;CAC/D,CAAC,CAAC;AAKH,+BAA+B;AAE/B,MAAM,CAAC,MAAM,kBAAkB,GAAG,CAAC,CAAC,MAAM,CAAC;IACzC,IAAI,EAAE,QAAQ;IACd,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,SAAS,CAAC;IAClC,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,KAAK,CAAC,cAAc,EAAE,4BAA4B,CAAC;IACpE,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,CAAC,WAAW,EAAE;CACrC,CAAC,CAAC;AAEH,MAAM,CAAC,MAAM,eAAe,GAAG,CAAC,CAAC,MAAM,CAAC;IACtC,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,IAAI,EAAE;IAC5B,KAAK,EAAE,CAAC,CAAC,KAAK,CAAC,kBAAkB,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,GAAG,CAAC;CACnD,CAAC,CAAC;AAIH,kCAAkC;AAElC,MAAM,CAAC,MAAM,oBAAoB,GAAG,CAAC,CAAC,MAAM,CAAC;IAC3C,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,IAAI,EAAE;IAC5B,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC,QAAQ,EAAE;IAC3C,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,QAAQ,EAAE;IACzC,OAAO,EAAE,CAAC,CAAC,IAAI,CAAC,CAAC,QAAQ,EAAE,YAAY,EAAE,iBAAiB,CAAC,CAAC,CAAC,QAAQ,EAAE;CACxE,CAAC,CAAC;AAIH,sCAAsC;AAEtC,MAAM,CAAC,MAAM,iBAAiB,GAAG,CAAC,CAAC,MAAM,CAAC;IACxC,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,IAAI,EAAE;IAC5B,KAAK,EAAE,CAAC,CAAC,KAAK,CAAC,QAAQ,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,GAAG,CAAC;CACzC,CAAC,CAAC;AAIH,mCAAmC;AAEnC,MAAM,CAAC,MAAM,eAAe,GAAG,CAAC,CAAC,MAAM,CAAC;IACtC,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,IAAI,EAAE;IAC5B,SAAS,EAAE,CAAC,CAAC,KAAK,CAAC,QAAQ,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC;CACzC,CAAC,CAAC"}

package/node_modules/@ultra-claude/shared/dist/index.d.ts

@@ -1,5 +1,5 @@
 export { createProjectSchema, updateProjectSchema, moveProjectSchema, type CreateProjectInput, type UpdateProjectInput, type MoveProjectInput, } from './api/schemas/projects.js';
-export { syncSectionsSchema, sectionItemSchema, syncFilesSchema, syncFileItemSchema, createSnapshotSchema, type SyncSectionsInput, type SectionItem, type SyncFilesInput, type CreateSnapshotInput, } from './api/schemas/sync.js';
+export { syncSectionsSchema, sectionItemSchema, syncFilesSchema, syncFileItemSchema, createSnapshotSchema, deleteFilesSchema, reconcileSchema, type SyncSectionsInput, type SectionItem, type SyncFilesInput, type CreateSnapshotInput, type DeleteFilesInput, type ReconcileInput, } from './api/schemas/sync.js';
 export { computeContentHash, verifyContentHash } from './hashing.js';
 export { parseMarkdownSections, generateSlug } from './sections.js';
 export type { SectionData, ManifestEntry, ProjectRegistryEntry, ProjectRegistry, AgentCredentials, } from './types.js';

package/node_modules/@ultra-claude/shared/dist/index.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAEA,OAAO,EACL,mBAAmB,EACnB,mBAAmB,EACnB,iBAAiB,EACjB,KAAK,kBAAkB,EACvB,KAAK,kBAAkB,EACvB,KAAK,gBAAgB,GACtB,MAAM,2BAA2B,CAAC;AAEnC,OAAO,EACL,kBAAkB,EAClB,iBAAiB,EACjB,eAAe,EACf,kBAAkB,EAClB,oBAAoB,EACpB,KAAK,iBAAiB,EACtB,KAAK,WAAW,EAChB,KAAK,cAAc,EACnB,KAAK,mBAAmB,GACzB,MAAM,uBAAuB,CAAC;AAE/B,OAAO,EAAE,kBAAkB,EAAE,iBAAiB,EAAE,MAAM,cAAc,CAAC;AAErE,OAAO,EAAE,qBAAqB,EAAE,YAAY,EAAE,MAAM,eAAe,CAAC;AAEpE,YAAY,EACV,WAAW,EACX,aAAa,EACb,oBAAoB,EACpB,eAAe,EACf,gBAAgB,GACjB,MAAM,YAAY,CAAC;AAEpB,OAAO,EAAE,EAAE,EAAE,GAAG,EAAE,KAAK,MAAM,EAAE,MAAM,aAAa,CAAC;AAEnD,OAAO,EACL,mBAAmB,EACnB,qBAAqB,EACrB,wBAAwB,EACxB,8BAA8B,EAC9B,KAAK,kBAAkB,EACvB,KAAK,eAAe,EACpB,KAAK,kBAAkB,EACvB,KAAK,wBAAwB,GAC9B,MAAM,8BAA8B,CAAC;AAEtC,OAAO,EACL,sBAAsB,EACtB,sBAAsB,EACtB,KAAK,gBAAgB,EACrB,KAAK,gBAAgB,EACrB,KAAK,YAAY,GAClB,MAAM,wBAAwB,CAAC;AAEhC,OAAO,EACL,0BAA0B,EAC1B,kBAAkB,EAClB,mBAAmB,EACnB,gBAAgB,EAChB,6BAA6B,EAC7B,KAAK,oBAAoB,EACzB,KAAK,YAAY,EACjB,KAAK,aAAa,EAClB,KAAK,UAAU,EACf,KAAK,uBAAuB,GAC7B,MAAM,4BAA4B,CAAC"}
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAEA,OAAO,EACL,mBAAmB,EACnB,mBAAmB,EACnB,iBAAiB,EACjB,KAAK,kBAAkB,EACvB,KAAK,kBAAkB,EACvB,KAAK,gBAAgB,GACtB,MAAM,2BAA2B,CAAC;AAEnC,OAAO,EACL,kBAAkB,EAClB,iBAAiB,EACjB,eAAe,EACf,kBAAkB,EAClB,oBAAoB,EACpB,iBAAiB,EACjB,eAAe,EACf,KAAK,iBAAiB,EACtB,KAAK,WAAW,EAChB,KAAK,cAAc,EACnB,KAAK,mBAAmB,EACxB,KAAK,gBAAgB,EACrB,KAAK,cAAc,GACpB,MAAM,uBAAuB,CAAC;AAE/B,OAAO,EAAE,kBAAkB,EAAE,iBAAiB,EAAE,MAAM,cAAc,CAAC;AAErE,OAAO,EAAE,qBAAqB,EAAE,YAAY,EAAE,MAAM,eAAe,CAAC;AAEpE,YAAY,EACV,WAAW,EACX,aAAa,EACb,oBAAoB,EACpB,eAAe,EACf,gBAAgB,GACjB,MAAM,YAAY,CAAC;AAEpB,OAAO,EAAE,EAAE,EAAE,GAAG,EAAE,KAAK,MAAM,EAAE,MAAM,aAAa,CAAC;AAEnD,OAAO,EACL,mBAAmB,EACnB,qBAAqB,EACrB,wBAAwB,EACxB,8BAA8B,EAC9B,KAAK,kBAAkB,EACvB,KAAK,eAAe,EACpB,KAAK,kBAAkB,EACvB,KAAK,wBAAwB,GAC9B,MAAM,8BAA8B,CAAC;AAEtC,OAAO,EACL,sBAAsB,EACtB,sBAAsB,EACtB,KAAK,gBAAgB,EACrB,KAAK,gBAAgB,EACrB,KAAK,YAAY,GAClB,MAAM,wBAAwB,CAAC;AAEhC,OAAO,EACL,0BAA0B,EAC1B,kBAAkB,EAClB,mBAAmB,EACnB,gBAAgB,EAChB,6BAA6B,EAC7B,KAAK,oBAAoB,EACzB,KAAK,YAAY,EACjB,KAAK,aAAa,EAClB,KAAK,UAAU,EACf,KAAK,uBAAuB,GAC7B,MAAM,4BAA4B,CAAC"}

package/node_modules/@ultra-claude/shared/dist/index.js

@@ -1,6 +1,6 @@
 // @ultra-claude/shared — shared types, API contracts, block parsing
 export { createProjectSchema, updateProjectSchema, moveProjectSchema, } from './api/schemas/projects.js';
-export { syncSectionsSchema, sectionItemSchema, syncFilesSchema, syncFileItemSchema, createSnapshotSchema, } from './api/schemas/sync.js';
+export { syncSectionsSchema, sectionItemSchema, syncFilesSchema, syncFileItemSchema, createSnapshotSchema, deleteFilesSchema, reconcileSchema, } from './api/schemas/sync.js';
 export { computeContentHash, verifyContentHash } from './hashing.js';
 export { parseMarkdownSections, generateSlug } from './sections.js';
 export { ok, err } from './result.js';

package/node_modules/@ultra-claude/shared/dist/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,oEAAoE;AAEpE,OAAO,EACL,mBAAmB,EACnB,mBAAmB,EACnB,iBAAiB,GAIlB,MAAM,2BAA2B,CAAC;AAEnC,OAAO,EACL,kBAAkB,EAClB,iBAAiB,EACjB,eAAe,EACf,kBAAkB,EAClB,oBAAoB,GAKrB,MAAM,uBAAuB,CAAC;AAE/B,OAAO,EAAE,kBAAkB,EAAE,iBAAiB,EAAE,MAAM,cAAc,CAAC;AAErE,OAAO,EAAE,qBAAqB,EAAE,YAAY,EAAE,MAAM,eAAe,CAAC;AAUpE,OAAO,EAAE,EAAE,EAAE,GAAG,EAAe,MAAM,aAAa,CAAC;AAEnD,OAAO,EACL,mBAAmB,EACnB,qBAAqB,EACrB,wBAAwB,EACxB,8BAA8B,GAK/B,MAAM,8BAA8B,CAAC;AAEtC,OAAO,EACL,sBAAsB,EACtB,sBAAsB,GAIvB,MAAM,wBAAwB,CAAC;AAEhC,OAAO,EACL,0BAA0B,EAC1B,kBAAkB,EAClB,mBAAmB,EACnB,gBAAgB,EAChB,6BAA6B,GAM9B,MAAM,4BAA4B,CAAC"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,oEAAoE;AAEpE,OAAO,EACL,mBAAmB,EACnB,mBAAmB,EACnB,iBAAiB,GAIlB,MAAM,2BAA2B,CAAC;AAEnC,OAAO,EACL,kBAAkB,EAClB,iBAAiB,EACjB,eAAe,EACf,kBAAkB,EAClB,oBAAoB,EACpB,iBAAiB,EACjB,eAAe,GAOhB,MAAM,uBAAuB,CAAC;AAE/B,OAAO,EAAE,kBAAkB,EAAE,iBAAiB,EAAE,MAAM,cAAc,CAAC;AAErE,OAAO,EAAE,qBAAqB,EAAE,YAAY,EAAE,MAAM,eAAe,CAAC;AAUpE,OAAO,EAAE,EAAE,EAAE,GAAG,EAAe,MAAM,aAAa,CAAC;AAEnD,OAAO,EACL,mBAAmB,EACnB,qBAAqB,EACrB,wBAAwB,EACxB,8BAA8B,GAK/B,MAAM,8BAA8B,CAAC;AAEtC,OAAO,EACL,sBAAsB,EACtB,sBAAsB,GAIvB,MAAM,wBAAwB,CAAC;AAEhC,OAAO,EACL,0BAA0B,EAC1B,kBAAkB,EAClB,mBAAmB,EACnB,gBAAgB,EAChB,6BAA6B,GAM9B,MAAM,4BAA4B,CAAC"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "ultraclaude-agent",
-  "version": "0.0.16",
+  "version": "0.0.17",
   "type": "module",
   "bin": {
     "ultraclaude-agent": "./dist/cli.js"

package/src/sync.ts

@@ -444,6 +444,90 @@ export async function createSnapshot(
   return true;
 }
 
+// --- Delete files ---
+
+/**
+ * Notify the server that specific files have been deleted from disk.
+ * Cleans up synced_files, document_sections, plans, and backlog entries.
+ */
+export async function deleteFiles(
+  projectId: string,
+  projectPath: string,
+  absoluteFilePaths: string[],
+  credentials: AgentCredentials,
+): Promise<boolean> {
+  const log = logger.child({ projectId, op: 'deleteFiles' });
+  const docDir = join(projectPath, 'documentation');
+
+  const relativePaths = absoluteFilePaths.map((p) => relative(docDir, p));
+
+  const payload = { projectId, files: relativePaths };
+  const idempotencyKey = crypto.randomUUID();
+
+  const result = await apiRequest('POST', '/api/sync/delete-files', payload, credentials, {
+    'Idempotency-Key': idempotencyKey,
+  });
+
+  if (!result.success || !result.data.ok) {
+    const reason = !result.success ? result.message : `HTTP ${result.data.status}`;
+    log.warn({ error: reason, files: relativePaths }, 'Delete-files request failed');
+    return false;
+  }
+
+  // Clear local cache entries for deleted files
+  const state = getOrCreateState(projectId);
+  for (const relPath of relativePaths) {
+    state.fileHashes.delete(relPath);
+    // Clear section hashes for this file
+    for (const key of state.sectionHashes.keys()) {
+      if (key.startsWith(`${relPath}#`)) {
+        state.sectionHashes.delete(key);
+      }
+    }
+  }
+
+  log.info({ count: relativePaths.length }, 'Files deleted on server');
+  return true;
+}
+
+// --- Reconcile ---
+
+/**
+ * Tell the server the full set of files currently on disk.
+ * Server prunes synced_files, plans, and backlog items not in this set.
+ */
+async function reconcile(
+  projectId: string,
+  activePaths: string[],
+  credentials: AgentCredentials,
+): Promise<void> {
+  const log = logger.child({ projectId, op: 'reconcile' });
+
+  const payload = { projectId, filePaths: activePaths };
+  const idempotencyKey = crypto.randomUUID();
+
+  const result = await apiRequest('POST', '/api/sync/reconcile', payload, credentials, {
+    'Idempotency-Key': idempotencyKey,
+  });
+
+  if (!result.success || !result.data.ok) {
+    const reason = !result.success ? result.message : `HTTP ${result.data.status}`;
+    log.warn({ error: reason }, 'Reconcile request failed — orphaned data may persist until next sync');
+    return;
+  }
+
+  const body = (await result.data.json()) as {
+    data: { prunedFiles: number; prunedPlans: number; prunedBacklogItems: number };
+  };
+  const { prunedFiles, prunedPlans, prunedBacklogItems } = body.data;
+
+  if (prunedFiles > 0 || prunedPlans > 0 || prunedBacklogItems > 0) {
+    log.info({ prunedFiles, prunedPlans, prunedBacklogItems }, 'Reconciliation pruned orphaned data');
+  } else {
+    log.debug('Reconciliation complete — no orphans found');
+  }
+}
+
 // --- Initial sync for a project ---
 
 export async function initialSync(
@@ -456,9 +540,10 @@ export async function initialSync(
 
   await loadManifestIntoCache(projectId, credentials);
 
-  // Walk documentation/ and sync all files
+  // Walk documentation/ and sync all files, collecting relative paths
   const { glob } = await import('node:fs/promises');
   const docDir = join(projectPath, 'documentation');
+  const activePaths: string[] = [];
 
   try {
     for await (const entry of glob(join(docDir, '**/*'), {})) {
@@ -466,8 +551,15 @@ export async function initialSync(
       if (!fileStat?.isFile()) continue;
       if (fileStat.size > MAX_FILE_SIZE) continue;
 
+      const relPath = relative(docDir, entry);
+      activePaths.push(relPath);
+
       await syncFile(projectId, projectPath, entry, credentials);
     }
+
+    // Reconcile: prune server-side data for files that no longer exist on disk
+    await reconcile(projectId, activePaths, credentials);
+
     log.info('Initial sync complete');
   } catch (err) {
     log.warn({ err }, 'Initial sync incomplete — will catch up via watcher');

package/src/watcher.ts

@@ -3,7 +3,7 @@
 
 import chokidar from 'chokidar';
 import { join, basename } from 'node:path';
-import { syncFile, initialSync, createSnapshot, pushVersionMetadata } from './sync.js';
+import { syncFile, deleteFiles, initialSync, createSnapshot, pushVersionMetadata } from './sync.js';
 import { logger } from './logger.js';
 import type { AgentCredentials } from '@ultra-claude/shared';
 
@@ -69,7 +69,12 @@ export function startProjectWatcher(options: ProjectWatcherOptions): ProjectWatc
     .on('add', handleChange)
     .on('change', handleChange)
     .on('unlink', (filePath) => {
-      log.info({ file: filePath }, 'File deleted — sections will be marked as removed on next sync');
+      log.info({ file: filePath }, 'File deleted — notifying server');
+      credentialsPromise
+        .then(creds => deleteFiles(projectId, projectPath, [filePath], creds))
+        .catch((deleteErr) => {
+          log.error({ err: deleteErr, file: filePath }, 'Delete notification failed for file');
+        });
     })
     .on('error', (err) => log.error({ err }, 'Documentation watcher error'))
     .on('ready', () => log.info('Documentation watcher ready'));