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/hooks/pre-commit.backup

@@ -1,24 +0,0 @@
-#!/usr/bin/env sh
-# bd-shim v1
-# bd-hooks-version: 0.52.0
-#
-# bd (beads) pre-commit hook - thin shim
-#
-# This shim delegates to 'bd hook pre-commit' which contains
-# the actual hook logic. This pattern ensures hook behavior is always
-# in sync with the installed bd version - no manual updates needed.
-#
-# The 'bd hook' command (singular) supports:
-# - Per-worktree export state tracking
-# - Dolt branch-then-merge pattern for cell-level conflict resolution
-# - Hook chaining configuration
-
-# Check if bd is available
-if ! command -v bd >/dev/null 2>&1; then
-    echo "Warning: bd command not found in PATH, skipping pre-commit hook" >&2
-    echo "  Install bd: brew install beads" >&2
-    echo "  Or add bd to your PATH" >&2
-    exit 0
-fi
-
-exec bd hook pre-commit "$@"