Refactor session ID references from sdk_session_id to memory_session_id across multiple services and database queries

- Updated SQL queries in cleanup-duplicates.ts and context-generator.ts to use memory_session_id.
- Modified interfaces in context-generator.ts to reflect the new session ID naming.
- Implemented a repair migration in SessionStore.ts to rename columns in existing tables.
- Adjusted FormattingService.ts and SDKAgent.ts to utilize memory_session_id for session handling.
- Ensured SearchManager.ts retrieves summaries and observations using the updated memory_session_id.

src/bin/cleanup-duplicates.ts

@@ -15,14 +15,14 @@ function main() {
   console.log('Finding duplicate observations...');
 
   const duplicateObsQuery = db['db'].prepare(`
-    SELECT sdk_session_id, title, subtitle, type, COUNT(*) as count, GROUP_CONCAT(id) as ids
+    SELECT memory_session_id, title, subtitle, type, COUNT(*) as count, GROUP_CONCAT(id) as ids
     FROM observations
-    GROUP BY sdk_session_id, title, subtitle, type
+    GROUP BY memory_session_id, title, subtitle, type
     HAVING count > 1
   `);
 
   const duplicateObs = duplicateObsQuery.all() as Array<{
-    sdk_session_id: string;
+    memory_session_id: string;
     title: string;
     subtitle: string;
     type: string;
@@ -50,14 +50,14 @@ function main() {
   console.log('\n\nFinding duplicate summaries...');
 
   const duplicateSumQuery = db['db'].prepare(`
-    SELECT sdk_session_id, request, completed, learned, COUNT(*) as count, GROUP_CONCAT(id) as ids
+    SELECT memory_session_id, request, completed, learned, COUNT(*) as count, GROUP_CONCAT(id) as ids
     FROM session_summaries
-    GROUP BY sdk_session_id, request, completed, learned
+    GROUP BY memory_session_id, request, completed, learned
     HAVING count > 1
   `);
 
   const duplicateSum = duplicateSumQuery.all() as Array<{
-    sdk_session_id: string;
+    memory_session_id: string;
     request: string;
     completed: string;
     learned: string;

src/services/context-generator.ts

@@ -122,7 +122,7 @@ const colors = {
 
 interface Observation {
   id: number;
-  sdk_session_id: string;
+  memory_session_id: string;
   type: string;
   title: string | null;
   subtitle: string | null;
@@ -138,7 +138,7 @@ interface Observation {
 
 interface SessionSummary {
   id: number;
-  sdk_session_id: string;
+  memory_session_id: string;
   request: string | null;
   investigated: string | null;
   learned: string | null;
@@ -246,7 +246,7 @@ export async function generateContext(input?: ContextInput, useColors: boolean =
   // Get recent observations
   const observations = db.db.prepare(`
     SELECT
-      id, sdk_session_id, type, title, subtitle, narrative,
+      id, memory_session_id, type, title, subtitle, narrative,
       facts, concepts, files_read, files_modified, discovery_tokens,
       created_at, created_at_epoch
     FROM observations
@@ -262,7 +262,7 @@ export async function generateContext(input?: ContextInput, useColors: boolean =
 
   // Get recent summaries
   const recentSummaries = db.db.prepare(`
-    SELECT id, sdk_session_id, request, investigated, learned, completed, next_steps, created_at, created_at_epoch
+    SELECT id, memory_session_id, request, investigated, learned, completed, next_steps, created_at, created_at_epoch
     FROM session_summaries
     WHERE project = ?
     ORDER BY created_at_epoch DESC
@@ -275,10 +275,10 @@ export async function generateContext(input?: ContextInput, useColors: boolean =
 
   if (config.showLastMessage && observations.length > 0) {
     const currentSessionId = input?.session_id;
-    const priorSessionObs = observations.find(obs => obs.sdk_session_id !== currentSessionId);
+    const priorSessionObs = observations.find(obs => obs.memory_session_id !== currentSessionId);
 
     if (priorSessionObs) {
-      const priorSessionId = priorSessionObs.sdk_session_id;
+      const priorSessionId = priorSessionObs.memory_session_id;
       const dashedCwd = cwdToDashed(cwd);
       const transcriptPath = path.join(homedir(), '.claude', 'projects', dashedCwd, `${priorSessionId}.jsonl`);
       const messages = extractPriorMessages(transcriptPath);

src/services/sqlite/SessionStore.ts

@@ -44,6 +44,7 @@ export class SessionStore {
     this.ensureDiscoveryTokensColumn();
     this.createPendingMessagesTable();
     this.renameSessionIdColumns();
+    this.repairSessionIdColumnRename();
   }
 
   /**
@@ -626,6 +627,75 @@ export class SessionStore {
     }
   }
 
+  /**
+   * Repair session ID column renames (migration 19)
+   * Migration 17 may have been recorded but failed to actually rename columns.
+   * This migration checks each table and renames if needed (idempotent).
+   */
+  private repairSessionIdColumnRename(): void {
+    try {
+      const applied = this.db.prepare('SELECT version FROM schema_versions WHERE version = ?').get(19) as SchemaVersion | undefined;
+      if (applied) return;
+
+      logger.info('DB', 'Checking session ID column renames (repair migration)');
+
+      let repairsNeeded = false;
+
+      // Check and fix sdk_sessions
+      const sessionsInfo = this.db.query('PRAGMA table_info(sdk_sessions)').all() as TableColumnInfo[];
+      if (sessionsInfo.some(col => col.name === 'claude_session_id')) {
+        logger.info('DB', 'Repairing sdk_sessions columns');
+        this.db.run('ALTER TABLE sdk_sessions RENAME COLUMN claude_session_id TO content_session_id');
+        this.db.run('ALTER TABLE sdk_sessions RENAME COLUMN sdk_session_id TO memory_session_id');
+        repairsNeeded = true;
+      }
+
+      // Check and fix pending_messages
+      const pendingInfo = this.db.query('PRAGMA table_info(pending_messages)').all() as TableColumnInfo[];
+      if (pendingInfo.some(col => col.name === 'claude_session_id')) {
+        logger.info('DB', 'Repairing pending_messages columns');
+        this.db.run('ALTER TABLE pending_messages RENAME COLUMN claude_session_id TO content_session_id');
+        repairsNeeded = true;
+      }
+
+      // Check and fix observations
+      const obsInfo = this.db.query('PRAGMA table_info(observations)').all() as TableColumnInfo[];
+      if (obsInfo.some(col => col.name === 'sdk_session_id')) {
+        logger.info('DB', 'Repairing observations columns');
+        this.db.run('ALTER TABLE observations RENAME COLUMN sdk_session_id TO memory_session_id');
+        repairsNeeded = true;
+      }
+
+      // Check and fix session_summaries
+      const summariesInfo = this.db.query('PRAGMA table_info(session_summaries)').all() as TableColumnInfo[];
+      if (summariesInfo.some(col => col.name === 'sdk_session_id')) {
+        logger.info('DB', 'Repairing session_summaries columns');
+        this.db.run('ALTER TABLE session_summaries RENAME COLUMN sdk_session_id TO memory_session_id');
+        repairsNeeded = true;
+      }
+
+      // Check and fix user_prompts
+      const promptsInfo = this.db.query('PRAGMA table_info(user_prompts)').all() as TableColumnInfo[];
+      if (promptsInfo.some(col => col.name === 'claude_session_id')) {
+        logger.info('DB', 'Repairing user_prompts columns');
+        this.db.run('ALTER TABLE user_prompts RENAME COLUMN claude_session_id TO content_session_id');
+        repairsNeeded = true;
+      }
+
+      // Record migration
+      this.db.prepare('INSERT OR IGNORE INTO schema_versions (version, applied_at) VALUES (?, ?)').run(19, new Date().toISOString());
+
+      if (repairsNeeded) {
+        logger.info('DB', 'Session ID column rename repairs completed');
+      } else {
+        logger.info('DB', 'No session ID column repairs needed');
+      }
+    } catch (error: any) {
+      logger.error('DB', 'Session ID column rename repair error', undefined, error);
+      throw error;
+    }
+  }
+
   /**
    * Update the memory session ID for a session
    * Called by SDKAgent when it captures the session ID from the first SDK message
@@ -1147,6 +1217,10 @@ export class SessionStore {
     const nowEpoch = now.getTime();
 
     // Pure INSERT OR IGNORE - no updates, no complexity
+    // NOTE: memory_session_id is initialized to contentSessionId as a placeholder for FK purposes.
+    // The REAL memory session ID is captured by SDKAgent from the first SDK response
+    // and stored via updateMemorySessionId(). The resume logic checks if memorySessionId
+    // differs from contentSessionId before using it - see SDKAgent.startSession().
     this.db.prepare(`
       INSERT OR IGNORE INTO sdk_sessions
       (content_session_id, memory_session_id, project, user_prompt, started_at, started_at_epoch, status)

src/services/worker/FormattingService.ts

@@ -74,7 +74,7 @@ Tips:
     const id = `#S${session.id}`;
     const time = this.formatTime(session.created_at_epoch);
     const icon = '🎯';
-    const title = session.request || `Session ${session.sdk_session_id?.substring(0, 8) || 'unknown'}`;
+    const title = session.request || `Session ${session.memory_session_id?.substring(0, 8) || 'unknown'}`;
 
     return `| ${id} | ${time} | ${icon} | ${title} | - | - |`;
   }
@@ -137,7 +137,7 @@ Tips:
     const id = `#S${session.id}`;
     const time = this.formatTime(session.created_at_epoch);
     const icon = '🎯';
-    const title = session.request || `Session ${session.sdk_session_id?.substring(0, 8) || 'unknown'}`;
+    const title = session.request || `Session ${session.memory_session_id?.substring(0, 8) || 'unknown'}`;
 
     // Use ditto mark if same time as previous row
     const timeDisplay = time === lastTime ? '″' : time;

src/services/worker/SDKAgent.ts

@@ -64,22 +64,29 @@ export class SDKAgent {
       // Create message generator (event-driven)
       const messageGenerator = this.createMessageGenerator(session);
 
+      // CRITICAL: Only resume if memorySessionId is a REAL captured SDK session ID,
+      // not the placeholder (which equals contentSessionId). The placeholder is set
+      // for FK purposes but would cause the bug where we try to resume the USER's session!
+      const hasRealMemorySessionId = session.memorySessionId &&
+        session.memorySessionId !== session.contentSessionId;
+
       logger.info('SDK', 'Starting SDK query', {
         sessionDbId: session.sessionDbId,
         contentSessionId: session.contentSessionId,
         memorySessionId: session.memorySessionId,
-        resume_parameter: session.memorySessionId || '(none - fresh start)',
+        hasRealMemorySessionId,
+        resume_parameter: hasRealMemorySessionId ? session.memorySessionId : '(none - fresh start)',
         lastPromptNumber: session.lastPromptNumber
       });
 
       // Run Agent SDK query loop
-      // Use memorySessionId for resume (captured from previous SDK response) if available
+      // Only resume if we have a REAL captured memory session ID (not the placeholder)
       const queryResult = query({
         prompt: messageGenerator,
         options: {
           model: modelId,
-          // Only resume if we have a captured memory session ID from previous SDK interaction
-          ...(session.memorySessionId && { resume: session.memorySessionId }),
+          // Only resume if memorySessionId differs from contentSessionId (meaning it was captured)
+          ...(hasRealMemorySessionId && { resume: session.memorySessionId }),
           disallowedTools,
           abortController: session.abortController,
           pathToClaudeCodeExecutable: claudePath

src/services/worker/SearchManager.ts

@@ -1376,13 +1376,13 @@ export class SearchManager {
         lines.push('');
 
         for (const session of sessions) {
-          if (!session.sdk_session_id) continue;
+          if (!session.memory_session_id) continue;
 
           lines.push('---');
           lines.push('');
 
           if (session.has_summary) {
-            const summary = this.sessionStore.getSummaryForSession(session.sdk_session_id);
+            const summary = this.sessionStore.getSummaryForSession(session.memory_session_id);
             if (summary) {
               const promptLabel = summary.prompt_number ? ` (Prompt #${summary.prompt_number})` : '';
               lines.push(`**Summary${promptLabel}**`);
@@ -1432,7 +1432,7 @@ export class SearchManager {
               lines.push(`**Request:** ${session.user_prompt}`);
             }
 
-            const observations = this.sessionStore.getObservationsForSession(session.sdk_session_id);
+            const observations = this.sessionStore.getObservationsForSession(session.memory_session_id);
             if (observations.length > 0) {
               lines.push('');
               lines.push(`**Observations (${observations.length}):**`);