feat(CF-580): Implement transcript-based session recovery for MCP

Add direct transcript ingestion and orphan recovery using Claude Code's JSONL
transcripts instead of relying on daemon-based note synchronization.

Changes:

1. **Database migration** (027_session_transcript_storage.sql):
   - Add transcript_jsonl, transcript_ingested_at, transcript_file_path columns
   - Add indexes for efficient ingestion tracking

2. **Transcript parser utility** (src/utils/transcript-parser.ts):
   - parseTranscriptFile(): Parse JSONL line-by-line, handle corrupt lines
   - encodeWorkingDir(): Convert paths to Claude Code directory encoding
   - findOrphanedTranscripts(): Scan for stale transcript files
   - ingestTranscriptToDatabase(): Main ingestion function for Node.js

3. **Orphan recovery enhancement** (src/tools/sessions.ts):
   - sessionRecoverOrphaned() now tries transcript ingestion first
   - Finds most recently modified JSONL in project directory
   - Falls back to legacy notes.md recovery for backward compatibility
   - Properly handles path encoding (/ and . → -)

Benefits:
- No daemon needed for recovery (Phase 2 will remove LaunchAgent)
- Full transcript audit trail stored in database
- Immediate recovery capability for orphaned sessions
- Cleaner architecture (no markdown parsing complexity)
- Compatible with Claude Code's UUID-based session files

Co-Authored-By: Claude Haiku 4.5 <noreply@anthropic.com>

src/tools/sessions.ts

@@ -488,8 +488,55 @@ export async function sessionRecoverOrphaned(args: { project?: string }): Promis
         `✓ Session ${session.project} #${session.session_number} marked as abandoned`
       );
 
-      // Attempt to recover notes from temp file
+      // Attempt to recover transcript first (CF-580)
+      let transcriptRecovered = false;
       if (session.working_directory) {
+        // Construct projects path: ~/.claude/projects/{encoded-dir}/
+        // Encoding: / and . → - (Claude Code removes dots from usernames)
+        const home = process.env.HOME || '';
+        const encodedDir = session.working_directory.replace(/[/\.]/g, '-');
+        const projectsDir = `${home}/.claude/projects/${encodedDir}`;
+
+        try {
+          const fs = await import('fs');
+          const path = await import('path');
+
+          if (fs.default.existsSync(projectsDir)) {
+            // Find the most recently modified JSONL file
+            const files = fs.default.readdirSync(projectsDir);
+            const jsonlFiles = files
+              .filter(f => f.endsWith('.jsonl'))
+              .map(f => ({
+                name: f,
+                path: `${projectsDir}/${f}`,
+                mtime: fs.default.statSync(`${projectsDir}/${f}`).mtimeMs,
+              }))
+              .sort((a, b) => b.mtime - a.mtime);
+
+            if (jsonlFiles.length > 0) {
+              const latestFile = jsonlFiles[0];
+              const transcriptContent = fs.default.readFileSync(latestFile.path, 'utf-8');
+              const lineCount = transcriptContent.split('\n').filter(l => l.trim()).length;
+
+              // Update session with transcript
+              await execute(
+                `UPDATE sessions
+                 SET transcript_jsonl = $1, transcript_ingested_at = NOW(), transcript_file_path = $2, updated_at = NOW()
+                 WHERE id = $3`,
+                [transcriptContent, latestFile.path, session.id]
+              );
+
+              results.push(`  → Recovered transcript (${lineCount} lines)`);
+              transcriptRecovered = true;
+            }
+          }
+        } catch (err) {
+          // Silently skip transcript recovery errors
+        }
+      }
+
+      // Fallback: Attempt to recover notes from temp file if transcript not recovered
+      if (!transcriptRecovered && session.working_directory) {
         const tempFilePath = `${session.working_directory}/.claude-session/${session.id}/notes.md`;
 
         try {
@@ -497,7 +544,7 @@ export async function sessionRecoverOrphaned(args: { project?: string }): Promis
           const recovered = await recoverNotesFromTempFile(session.id, tempFilePath, 'recovered');
 
           if (recovered > 0) {
-            results.push(`  → Recovered ${recovered} note(s) from temp file`);
+            results.push(`  → Recovered ${recovered} note(s) from temp file (legacy)`);
             totalNotesRecovered += recovered;
           }
         } catch (err) {