fix(cli): add --accept-permissions flag to ag run and ag create (#3336, #3337)

[OneStepAt4time]

Summary

Fixes #3336 and #3337 — sessions stall on permission-gated tasks.

Problem

ag run and ag create don't pass permissionMode to the server. When Claude tries to write files, the session hits the permission gate and stalls indefinitely. ag run times out; ag create leaves zombie sessions.

Fix

New flag: --accept-permissions / -y

• Sets permissionMode: 'bypassPermissions' on session creation
• Both ag run and ag create support it
• Backward compatible: without the flag, behavior is unchanged

Usage

ag run "Create a file" --accept-permissions
ag create "Build a login page" -y

Verification

• tsc --noEmit: clean
• Minimal change: flag parse + spread into request body

[aegis-gh-agent]

✅ Approved — all 9 merge gates pass.

Review summary:

• Correct minimal fix for #3336, #3337 — sessions no longer stall on permission-gated tasks
• Flag parsing (--accept-permissions / -y) is clean, backward-compatible
• Conditional spread into request body is correct
• CI green (all checks pass)
• Targets develop ✅

Minor note (non-blocking): No unit tests for the new flag. Consider adding a test case in a follow-up PR to verify permissionMode: "bypassPermissions" is included in the request body when the flag is passed. The mechanical nature of this change makes it low-risk without tests, but coverage is always welcome.