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/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) {