@noesis-brain/mcp-server 2.1.0 → 2.1.2

package/dist/tools/index.js

@@ -13,6 +13,7 @@ import { initEmbeddingService, generateEmbedding, generateEmbeddingsBatch } from
 import { SyncStateManager, determineSyncDirection } from './SyncStateManager.js';
 import { registerNaviTools } from './navis.js';
 import { registerBacklogTools } from './backlog.js';
+import { registerExamTools } from './exam.js';
 import { suggestOtherOsPath } from '../utils/suggestPath.js';
 import { diff3Merge, diffPatch } from 'node-diff3';
 // ============================================
@@ -185,6 +186,7 @@ export function registerTools(server, services) {
     // Register Navi management tools
     registerNaviTools(server, client);
     registerBacklogTools(server, client);
+    registerExamTools(server, client);
     // Register search_notes tool
     server.tool('search_notes', 'Search your knowledge base using full-text search. Returns relevant notes ranked by BM25 relevance.', {
         query: z.string().describe('Search query (natural language or keywords)'),
@@ -1390,20 +1392,27 @@ export function registerTools(server, services) {
                                             keywords: cloudKw.length > 0 ? cloudKw : undefined
                                         })
                                         : mergedContent;
-                                    const enrichedHash = NoesisClient.computeHash(enrichedContent);
-                                    const mergedFile = {
-                                        ...localFile,
-                                        content: enrichedContent,
-                                        hash: enrichedHash
-                                    };
-                                    // preserveMetadata=true: keep cloud's AI-generated title/description/keywords
-                                    await client.upsertNote(mergedFile, metadata, { force: true, regenerateMetadata, preserveMetadata: true });
-                                    // Write enriched content back to local file
-                                    const localPath = path.join(syncRoot.path, relativePath);
-                                    fs.writeFileSync(localPath, enrichedContent, 'utf-8');
-                                    stateMgr.setBaseline(relativePath, { hash: enrichedHash, lastSyncedAt: new Date().toISOString() }, enrichedContent);
-                                    result.details.push({ file: relativePath, action: 'pushed_update', reason: 'merged' });
-                                    result.pushed.updated++;
+                                    // Safety net: never silently destroy content on merge (see per-file branch).
+                                    if (enrichedContent.length < localFile.content.length * 0.5 && localFile.content.length > 2048) {
+                                        const lost = Math.round(100 * (1 - enrichedContent.length / localFile.content.length));
+                                        result.errors.push(`Skipped push for ${relativePath}: merge would drop ${lost}% of content (${localFile.content.length}->${enrichedContent.length} bytes). Left unchanged to avoid data loss.`);
+                                    }
+                                    else {
+                                        const enrichedHash = NoesisClient.computeHash(enrichedContent);
+                                        const mergedFile = {
+                                            ...localFile,
+                                            content: enrichedContent,
+                                            hash: enrichedHash
+                                        };
+                                        // preserveMetadata=true: keep cloud's AI-generated title/description/keywords
+                                        await client.upsertNote(mergedFile, metadata, { force: true, regenerateMetadata, preserveMetadata: true });
+                                        // Write enriched content back to local file
+                                        const localPath = path.join(syncRoot.path, relativePath);
+                                        fs.writeFileSync(localPath, enrichedContent, 'utf-8');
+                                        stateMgr.setBaseline(relativePath, { hash: enrichedHash, lastSyncedAt: new Date().toISOString() }, enrichedContent);
+                                        result.details.push({ file: relativePath, action: 'pushed_update', reason: 'merged' });
+                                        result.pushed.updated++;
+                                    }
                                 }
                             }
                             else if (direction === 'pull') {
@@ -3051,26 +3060,35 @@ export async function syncSpecificFiles(filePaths, dryRun, client, force = false
                                 keywords: cloudKw.length > 0 ? cloudKw : undefined
                             })
                             : mergedContent;
-                        const enrichedHash = NoesisClient.computeHash(enrichedContent);
-                        const localFile = {
-                            path: normalizedPath,
-                            relativePath,
-                            content: enrichedContent,
-                            hash: enrichedHash,
-                            mtime: stats.mtime,
-                            size: stats.size,
-                            rootId: matchingRoot.id,
-                            rootName: matchingRoot.name,
-                            project
-                        };
-                        // preserveMetadata=true: keep cloud's AI-generated title/description/keywords
-                        await client.upsertNote(localFile, localMetadata, { force: true, regenerateMetadata, preserveMetadata: true });
-                        // Write enriched content back to local file
-                        fs.writeFileSync(normalizedPath, enrichedContent, 'utf-8');
-                        stateMgr.setBaseline(relativePath, { hash: enrichedHash, lastSyncedAt: new Date().toISOString() }, enrichedContent);
-                        result.details.push({ file: relativePath, action: 'pushed_update', reason: 'merged' });
-                        result.pushed.updated++;
-                        affectedRoots.add(matchingRoot.id);
+                        // Safety net: a merge must never silently destroy content. If the merged
+                        // result lost most of the local body, abort this file's push instead of
+                        // overwriting local + cloud with a truncated note.
+                        if (enrichedContent.length < localContent.length * 0.5 && localContent.length > 2048) {
+                            const lost = Math.round(100 * (1 - enrichedContent.length / localContent.length));
+                            result.errors.push(`Skipped push for ${relativePath}: merge would drop ${lost}% of content (${localContent.length}->${enrichedContent.length} bytes). Left unchanged to avoid data loss.`);
+                        }
+                        else {
+                            const enrichedHash = NoesisClient.computeHash(enrichedContent);
+                            const localFile = {
+                                path: normalizedPath,
+                                relativePath,
+                                content: enrichedContent,
+                                hash: enrichedHash,
+                                mtime: stats.mtime,
+                                size: stats.size,
+                                rootId: matchingRoot.id,
+                                rootName: matchingRoot.name,
+                                project
+                            };
+                            // preserveMetadata=true: keep cloud's AI-generated title/description/keywords
+                            await client.upsertNote(localFile, localMetadata, { force: true, regenerateMetadata, preserveMetadata: true });
+                            // Write enriched content back to local file
+                            fs.writeFileSync(normalizedPath, enrichedContent, 'utf-8');
+                            stateMgr.setBaseline(relativePath, { hash: enrichedHash, lastSyncedAt: new Date().toISOString() }, enrichedContent);
+                            result.details.push({ file: relativePath, action: 'pushed_update', reason: 'merged' });
+                            result.pushed.updated++;
+                            affectedRoots.add(matchingRoot.id);
+                        }
                     }
                 }
                 else if (direction === 'pull') {
@@ -3185,22 +3203,36 @@ export async function syncSpecificFiles(filePaths, dryRun, client, force = false
             }]
     };
 }
+/**
+ * Split leading YAML frontmatter from a markdown document.
+ *
+ * The opening `---` must be the very first line and the closing `---` must be on its
+ * own line (line-anchored). This deliberately does NOT use `indexOf('---', 3)`: a bare
+ * substring search matches a `---` inside a frontmatter value, a `---`/`----` thematic
+ * break in the body, or a `---` inside a code fence — which previously caused notes to
+ * be truncated / their frontmatter duplicated on sync.
+ *
+ * @returns raw = whole matched block incl. fences + trailing newline; inner = the YAML
+ *          between the fences; body = everything after the block. If there is no valid
+ *          leading frontmatter, raw/inner are '' and body is the full content.
+ */
+export function splitFrontmatter(content) {
+    const m = content.match(/^---[ \t]*\r?\n([\s\S]*?)\r?\n---[ \t]*(?:\r?\n|$)/);
+    if (!m)
+        return { raw: '', inner: '', body: content };
+    return { raw: m[0], inner: m[1], body: content.slice(m[0].length) };
+}
 /**
  * Parse YAML frontmatter from markdown content using js-yaml
  */
 function parseYamlFrontmatter(content) {
     const result = {};
-    // Check for YAML frontmatter (--- at start)
-    if (!content.startsWith('---')) {
-        return result;
-    }
-    const endIndex = content.indexOf('---', 3);
-    if (endIndex === -1) {
+    const { inner } = splitFrontmatter(content);
+    if (!inner) {
         return result;
     }
-    const frontmatterStr = content.substring(3, endIndex).trim();
     try {
-        const parsed = yaml.load(frontmatterStr);
+        const parsed = yaml.load(inner);
         if (!parsed || typeof parsed !== 'object') {
             return result;
         }
@@ -3248,9 +3280,14 @@ function parseCloudKeywords(keywords) {
  * Update frontmatter in file content with new metadata values
  * Preserves existing frontmatter structure and only updates specified fields
  */
-function updateFrontmatter(content, updates) {
-    // If no frontmatter exists, create one
-    if (!content.startsWith('---')) {
+export function updateFrontmatter(content, updates) {
+    const { inner, body } = splitFrontmatter(content);
+    // If no (valid) frontmatter exists, create one
+    if (!inner) {
+        if (content.startsWith('---')) {
+            // Opens with a fence but has no valid closing fence: don't risk mangling it.
+            return content;
+        }
         const frontmatterLines = ['---'];
         if (updates.title)
             frontmatterLines.push(`title: ${updates.title}`);
@@ -3265,13 +3302,8 @@ function updateFrontmatter(content, updates) {
         frontmatterLines.push('---');
         return frontmatterLines.join('\n') + '\n' + content;
     }
-    // Find end of frontmatter
-    const endIndex = content.indexOf('---', 3);
-    if (endIndex === -1) {
-        return content; // Invalid frontmatter, return unchanged
-    }
-    const frontmatter = content.substring(3, endIndex);
-    const bodyContent = content.substring(endIndex + 3);
+    const frontmatter = inner;
+    const bodyContent = body;
     const lines = frontmatter.split(/\r?\n/);
     const newLines = [];
     const updatedKeys = new Set();
@@ -3334,31 +3366,27 @@ function updateFrontmatter(content, updates) {
             newLines.push(`  - ${kw}`);
         }
     }
-    return '---\n' + newLines.filter(l => l.trim() !== '').join('\n') + '\n---' + bodyContent;
+    return '---\n' + newLines.filter(l => l.trim() !== '').join('\n') + '\n---\n' + bodyContent;
 }
 /**
  * Parse markdown content into structure: frontmatter, H1 heading, and body
  */
-function parseMarkdownStructure(content) {
-    let frontmatter = '';
-    let remaining = content;
-    // Extract YAML frontmatter (--- ... ---)
-    if (content.startsWith('---')) {
-        const endIndex = content.indexOf('---', 3);
-        if (endIndex !== -1) {
-            frontmatter = content.substring(0, endIndex + 3);
-            remaining = content.substring(endIndex + 3).replace(/^\r?\n/, ''); // Remove leading newline after frontmatter
-        }
-    }
-    // Extract first H1 heading (# ...)
-    const h1Match = remaining.match(/^(#\s+.+?)(\r?\n|$)/m);
+export function parseMarkdownStructure(content) {
+    // Extract YAML frontmatter (line-anchored; see splitFrontmatter).
+    const { raw, body: afterFrontmatter } = splitFrontmatter(content);
+    const frontmatter = raw ? raw.replace(/\r?\n$/, '') : ''; // keep fences; reconstruct re-adds the trailing newline
+    const remaining = afterFrontmatter;
+    // Extract the note's H1 heading — ONLY when it is the first non-blank line of the
+    // body. A non-anchored /m search would match a `# ...` line inside a fenced code
+    // block (e.g. a shell comment) and set body to everything after it, silently
+    // dropping the whole note above it. Anchoring to the start keeps all content.
+    const h1Match = remaining.match(/^\s*(#[ \t]+.+?)(\r?\n|$)/);
     let h1 = null;
     let body = remaining;
     if (h1Match) {
         h1 = h1Match[1];
-        // Get everything after the H1 (including the newline after it)
-        const h1EndIndex = remaining.indexOf(h1Match[0]) + h1Match[0].length;
-        body = remaining.substring(h1EndIndex);
+        // Everything after the matched leading H1 line becomes the body.
+        body = remaining.substring(h1Match[0].length);
     }
     return { frontmatter, h1, body };
 }
@@ -3628,7 +3656,7 @@ async function runConflictCascade(opts) {
  * Merge local content with cloud content
  * Strategy: Cloud's H1 wins (Noesis edits), Local's body wins (local edits)
  */
-function mergeContent(localContent, cloudContent) {
+export function mergeContent(localContent, cloudContent) {
     const localParsed = parseMarkdownStructure(localContent);
     const cloudParsed = parseMarkdownStructure(cloudContent);
     // Use cloud's H1 if it exists and differs from local, otherwise use local's H1