Integrate remaining agent merge PRs

[jasonsuhari]

Problem:
Several older dirty merge PRs remain open after main moved forward through later behavior changes.

Requested behavior:
Integrate PRs #69, #71, #72, #73, and #77 into a fresh batch branch based on latest origin/main, without pulling in newer PRs #82, #83, or #84 unless already on main.

Acceptance checks:

• Preserve origin/main behavior from Integrate quiet output badges #74, refactor: remove stale saved setup schema #80, and Add agent control tools #81.
• Preserve the intended feature behavior from PRs feat: integrate session resume #69, feat: integrate hidden manager groups #71, Integrate idle todo prompts #72, feat: integrate native auth manager #73, and feat: integrate dedicated command bar #77.
• Run cargo fmt, cargo check, and npm test where possible.
• Push the batch branch and open a PR to main.