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.

cmd/bd/setup/utils.go

@@ -0,0 +1,70 @@
+package setup
+
+import (
+	"fmt"
+	"os"
+	"path/filepath"
+)
+
+// atomicWriteFile writes data to a file atomically using a unique temporary file.
+// This prevents race conditions when multiple processes write to the same file.
+func atomicWriteFile(path string, data []byte, perm os.FileMode) error {
+	dir := filepath.Dir(path)
+
+	// Create unique temp file in same directory
+	tmpFile, err := os.CreateTemp(dir, ".*.tmp")
+	if err != nil {
+		return fmt.Errorf("create temp file: %w", err)
+	}
+	tmpPath := tmpFile.Name()
+
+	// Write data
+	if _, err := tmpFile.Write(data); err != nil {
+		_ = tmpFile.Close()    // best effort cleanup
+		_ = os.Remove(tmpPath) // best effort cleanup
+		return fmt.Errorf("write temp file: %w", err)
+	}
+
+	// Close temp file
+	if err := tmpFile.Close(); err != nil {
+		_ = os.Remove(tmpPath) // Best effort cleanup
+		return fmt.Errorf("close temp file: %w", err)
+	}
+
+	// Set permissions
+	if err := os.Chmod(tmpPath, perm); err != nil {
+		_ = os.Remove(tmpPath) // Best effort cleanup
+		return fmt.Errorf("set permissions: %w", err)
+	}
+
+	// Atomic rename
+	if err := os.Rename(tmpPath, path); err != nil {
+		_ = os.Remove(tmpPath) // Best effort cleanup
+		return fmt.Errorf("rename temp file: %w", err)
+	}
+
+	return nil
+}
+
+// DirExists checks if a directory exists
+func DirExists(path string) bool {
+	info, err := os.Stat(path)
+	return err == nil && info.IsDir()
+}
+
+// FileExists checks if a file exists
+func FileExists(path string) bool {
+	info, err := os.Stat(path)
+	return err == nil && !info.IsDir()
+}
+
+// EnsureDir creates a directory if it doesn't exist
+func EnsureDir(path string, perm os.FileMode) error {
+	if DirExists(path) {
+		return nil
+	}
+	if err := os.MkdirAll(path, perm); err != nil {
+		return fmt.Errorf("create directory: %w", err)
+	}
+	return nil
+}