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>

plugin/ui/viewer.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;
     }