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/templates/research-and-discovery.json

@@ -1,18 +0,0 @@
-{
-  "id": "research-and-discovery",
-  "name": "Research and Discovery",
-  "description": "",
-  "team": [
-    {
-      "archetypeId": "investigator",
-      "count": 1
-    },
-    {
-      "archetypeId": "architect",
-      "count": 1
-    }
-  ],
-  "createdAt": "2026-02-26T18:13:26.028Z",
-  "updatedAt": "2026-02-26T18:13:26.028Z",
-  "isBuiltIn": false
-}