fix(worktree): address CodeRabbit PR review feedback

- Document --branch override in npx-cli help text
- Guard ContextBuilder against empty projects[] override; fall back to cwd-derived primary
- Ensure merged_into_project indexes are created even if ALTER ran in a prior partial migration
- Reject adopt --branch/--cwd flags with missing or flag-like values
- Use defined --color-border-primary token for merged badge border

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

src/npx-cli/index.ts

@@ -52,7 +52,7 @@ ${pc.bold('Runtime Commands')} (requires Bun, delegates to installed plugin):
   ${pc.cyan('npx claude-mem restart')}              Restart worker service
   ${pc.cyan('npx claude-mem status')}               Show worker status
   ${pc.cyan('npx claude-mem search <query>')}       Search observations
-  ${pc.cyan('npx claude-mem adopt [--dry-run]')}    Stamp merged worktrees into parent project
+  ${pc.cyan('npx claude-mem adopt [--dry-run] [--branch <name>]')}    Stamp merged worktrees into parent project
   ${pc.cyan('npx claude-mem transcript watch')}     Start transcript watcher
 
 ${pc.bold('IDE Identifiers')}:

src/services/context/ContextBuilder.ts

@@ -136,8 +136,8 @@ export async function generateContext(
   // `project` (used for header + single-project query) is always the last entry
   // of `projects` so the empty-state header and the query target stay in sync
   // when a caller passes `projects` without a matching cwd (e.g. worker route).
-  const projects = input?.projects ?? context.allProjects;
-  const project = projects[projects.length - 1];
+  const projects = input?.projects?.length ? input.projects : context.allProjects;
+  const project = projects[projects.length - 1] ?? context.primary;
 
   // Full mode: fetch all observations but keep normal rendering (level 1 summaries)
   if (input?.full) {

src/services/sqlite/migrations/runner.ts

@@ -937,19 +937,19 @@ export class MigrationRunner {
       .all() as TableColumnInfo[];
     if (!obsCols.some(c => c.name === 'merged_into_project')) {
       this.db.run('ALTER TABLE observations ADD COLUMN merged_into_project TEXT');
-      this.db.run(
-        'CREATE INDEX IF NOT EXISTS idx_observations_merged_into ON observations(merged_into_project)'
-      );
     }
+    this.db.run(
+      'CREATE INDEX IF NOT EXISTS idx_observations_merged_into ON observations(merged_into_project)'
+    );
 
     const sumCols = this.db
       .query('PRAGMA table_info(session_summaries)')
       .all() as TableColumnInfo[];
     if (!sumCols.some(c => c.name === 'merged_into_project')) {
       this.db.run('ALTER TABLE session_summaries ADD COLUMN merged_into_project TEXT');
-      this.db.run(
-        'CREATE INDEX IF NOT EXISTS idx_summaries_merged_into ON session_summaries(merged_into_project)'
-      );
     }
+    this.db.run(
+      'CREATE INDEX IF NOT EXISTS idx_summaries_merged_into ON session_summaries(merged_into_project)'
+    );
   }
 }

src/services/worker-service.ts

@@ -1211,11 +1211,21 @@ async function main() {
     case 'adopt': {
       const dryRun = process.argv.includes('--dry-run');
       const branchIndex = process.argv.indexOf('--branch');
-      const onlyBranch = branchIndex !== -1 ? process.argv[branchIndex + 1] : undefined;
+      const branchValue = branchIndex !== -1 ? process.argv[branchIndex + 1] : undefined;
+      if (branchIndex !== -1 && (!branchValue || branchValue.startsWith('--'))) {
+        console.error('Usage: adopt [--dry-run] [--branch <branch>] [--cwd <path>]');
+        process.exit(1);
+      }
+      const onlyBranch = branchValue;
       // Honor an explicit --cwd override so the NPX CLI can pass through the
       // user's working directory (the spawn sets cwd to the marketplace dir).
       const cwdIndex = process.argv.indexOf('--cwd');
-      const repoPath = cwdIndex !== -1 ? process.argv[cwdIndex + 1] : process.cwd();
+      const cwdValue = cwdIndex !== -1 ? process.argv[cwdIndex + 1] : undefined;
+      if (cwdIndex !== -1 && (!cwdValue || cwdValue.startsWith('--'))) {
+        console.error('Usage: adopt [--dry-run] [--branch <branch>] [--cwd <path>]');
+        process.exit(1);
+      }
+      const repoPath = cwdValue ?? process.cwd();
 
       const result = await adoptMergedWorktrees({ repoPath, dryRun, onlyBranch });
 

src/ui/viewer-template.html

@@ -1139,7 +1139,7 @@
       letter-spacing: 0.02em;
       color: var(--color-text-muted);
       background: var(--color-type-badge-bg);
-      border: 1px solid var(--color-border);
+      border: 1px solid var(--color-border-primary);
       opacity: 0.85;
     }