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/dep_help.txt

@@ -1,42 +0,0 @@
-Manage dependencies between issues.
-
-When called with an issue ID and --blocks flag, creates a blocking dependency:
-  bd dep <blocker-id> --blocks <blocked-id>
-
-This is equivalent to:
-  bd dep add <blocked-id> <blocker-id>
-
-Examples:
-  bd dep bd-xyz --blocks bd-abc    # bd-xyz blocks bd-abc
-  bd dep add bd-abc bd-xyz         # Same as above (bd-abc depends on bd-xyz)
-
-Usage:
-  bd dep [issue-id] [flags]
-  bd dep [command]
-
-Available Commands:
-  add         Add a dependency
-  cycles      Detect dependency cycles
-  list        List dependencies or dependents of an issue
-  relate      Create a bidirectional relates_to link between issues
-  remove      Remove a dependency
-  tree        Show dependency tree
-  unrelate    Remove a relates_to link between issues
-
-Flags:
-  -b, --blocks string   Issue ID that this issue blocks (shorthand for: bd dep add <blocked> <blocker>)
-  -h, --help            help for dep
-
-Global Flags:
-      --actor string              Actor name for audit trail (default: $BD_ACTOR, git user.name, $USER)
-      --allow-stale               Allow operations on potentially stale data (skip staleness check)
-      --db string                 Database path (default: auto-discover .beads/*.db)
-      --dolt-auto-commit string   Dolt auto-commit policy (off|on|batch). 'on': commit after each write. 'batch': defer commits to bd sync / bd dolt commit; uncommitted changes persist in the working set until then. SIGTERM/SIGHUP flush pending batch commits. Default: off. Override via config key dolt.auto-commit
-      --json                      Output in JSON format
-      --profile                   Generate CPU profile for performance analysis
-  -q, --quiet                     Suppress non-essential output (errors only)
-      --readonly                  Read-only mode: block write operations (for worker sandboxes)
-      --sandbox                   Sandbox mode: disables auto-sync
-  -v, --verbose                   Enable verbose/debug output
-
-Use "bd dep [command] --help" for more information about a command.