feat: add context optimization features for AI agents (#297)

* feat: add bd prime and setup commands for AI agent integration

This commit consolidates context optimization features for AI agents:

## New Commands

**bd prime** - AI-optimized workflow context injection
- Outputs ~1-2k tokens of workflow context
- Context-aware: adapts to MCP vs CLI mode
- MCP mode: minimal reminders (~500 tokens)
- CLI mode: full command reference (~1-2k tokens)
- Warns against TodoWrite tool and markdown TODOs
- Designed for SessionStart/PreCompact hooks

**bd setup claude** - Claude Code integration installer
- Installs hooks via JSON configuration (not file scripts)
- Supports --project for project-only installation
- Supports --check to verify installation
- Supports --remove to uninstall hooks
- Idempotent (safe to run multiple times)
- Merges with existing settings

**bd setup cursor** - Cursor IDE integration installer
- Creates .cursor/rules/beads.mdc with workflow rules
- Simplified implementation (just overwrites file)

## bd doctor Enhancements

- New: CheckClaude() verifies Claude Code integration
- Detects plugin, MCP server, and hooks installation
- Provides actionable fix suggestions
- Extracted legacy pattern detection to doctor/legacy.go
- Detects JSONL-only mode and warns about legacy issues.jsonl

## Core Improvements

- FindBeadsDir() utility for cross-platform .beads/ discovery
- Works in JSONL-only mode (no database required)
- Sorted noDbCommands alphabetically (one per line for easy diffs)

## Testing

- Unit tests for setup command hook manipulation
- Tests for idempotency, adding/removing hooks
- All tests passing

## Documentation

- cmd/bd/doctor/claude.md - Documents why beads doesn't use Claude Skills
- commands/prime.md - Slash command for bd prime
- Fixed G304 gosec warnings with nosec comments

## Token Efficiency

The bd prime approach reduces AI context usage dramatically:
- MCP mode: ~500 tokens (vs ~10.5k for full MCP tool scan)
- CLI mode: ~1-2k tokens
- 80-99% reduction in standing context overhead

* fix: resolve linting errors in setup utils and remove obsolete test

- Add error check for tmpFile.Close() in setup/utils.go to fix golangci-lint G104
- Remove TestCheckMultipleJSONLFiles test that referenced deleted checkMultipleJSONLFiles function

Fixes golangci-lint errcheck violations introduced in the bd prime/setup feature.

internal/beads/beads.go

@@ -192,6 +192,34 @@ func FindDatabasePath() string {
 	return ""
 }
 
+// FindBeadsDir finds the .beads/ directory in the current directory tree
+// Returns empty string if not found. Supports both database and JSONL-only mode.
+// This is useful for commands that need to detect beads projects without requiring a database.
+func FindBeadsDir() string {
+	// 1. Check BEADS_DIR environment variable (preferred)
+	if beadsDir := os.Getenv("BEADS_DIR"); beadsDir != "" {
+		absBeadsDir := utils.CanonicalizePath(beadsDir)
+		if info, err := os.Stat(absBeadsDir); err == nil && info.IsDir() {
+			return absBeadsDir
+		}
+	}
+
+	// 2. Search for .beads/ in current directory and ancestors
+	cwd, err := os.Getwd()
+	if err != nil {
+		return ""
+	}
+
+	for dir := cwd; dir != "/" && dir != "."; dir = filepath.Dir(dir) {
+		beadsDir := filepath.Join(dir, ".beads")
+		if info, err := os.Stat(beadsDir); err == nil && info.IsDir() {
+			return beadsDir
+		}
+	}
+
+	return ""
+}
+
 // FindJSONLPath returns the expected JSONL file path for the given database path.
 // It searches for existing *.jsonl files in the database directory and returns
 // the first one found, or defaults to "issues.jsonl".