chore: Remove runtime artifacts from git tracking

This commit removes the following directories from git tracking (not from disk):
- .agent/ - AI tool configs
- .agents/ - Agent skills
- .augment/ - Augment AI
- .beads/ - Runtime database
- .claude/ - Claude AI configs
- .cline/ - Cline AI configs
- .openhands/ - OpenHands AI
- .dolt/ - Dolt database

These are now properly gitignored and will not appear in the repository.
This is a MASSIVE cleanup removing 1500+ files from version control.

.beads/.beads.bak/daemon-error

@@ -1,16 +0,0 @@
-
-LEGACY DATABASE DETECTED!
-
-This database was created before version 0.17.5 and lacks a repository fingerprint.
-To continue using this database, you must explicitly set its repository ID:
-
-  bd migrate --update-repo-id
-
-This ensures the database is bound to this repository and prevents accidental
-database sharing between different repositories.
-
-If this is a fresh clone, run:
-  rm -rf .beads && bd init
-
-Note: Auto-claiming legacy databases is intentionally disabled to prevent
-silent corruption when databases are copied between repositories.