DOCTOR IMPROVEMENTS: visual improvements/grouping + add comprehensive tests + fix gosec warnings (#656)

* test(doctor): add comprehensive tests for fix and check functions

Add edge case tests, e2e tests, and improve test coverage for:
- database_test.go: database integrity and sync checks
- git_test.go: git hooks, merge driver, sync branch tests
- gitignore_test.go: gitignore validation
- prefix_test.go: ID prefix handling
- fix/fix_test.go: fix operations
- fix/e2e_test.go: end-to-end fix scenarios
- fix/fix_edge_cases_test.go: edge case handling

* docs: add testing philosophy and anti-patterns guide

- Create TESTING_PHILOSOPHY.md covering test pyramid, priority matrix,
  what NOT to test, and 5 anti-patterns with code examples
- Add cross-reference from README_TESTING.md
- Document beads-specific guidance (well-covered areas vs gaps)
- Include target metrics (test-to-code ratio, execution time targets)

* chore: revert .beads/ to upstream/main state

* refactor(doctor): add category grouping and Ayu theme colors

- Add Category field to DoctorCheck for organizing checks by type
- Define category constants: Core, Git, Runtime, Data, Integration, Metadata
- Update thanks command to use shared Ayu color palette from internal/ui
- Simplify test fixtures by removing redundant test cases

* fix(doctor): prevent test fork bomb and fix test failures

- Add ErrTestBinary guard in getBdBinary() to prevent tests from
  recursively executing the test binary when calling bd subcommands
- Update claude_test.go to use new check names (CLI Availability,
  Prime Documentation)
- Fix syncbranch test path comparison by resolving symlinks
  (/var vs /private/var on macOS)
- Fix permissions check to use exact comparison instead of bitmask
- Fix UntrackedJSONL to use git commit --only to preserve staged changes
- Fix MergeDriver edge case test by making both .git dir and config
  read-only
- Add skipIfTestBinary helper for E2E tests that need real bd binary

* test(doctor): skip read-only config test in CI environments

GitHub Actions containers may have CAP_DAC_OVERRIDE or similar
capabilities that allow writing to read-only files, causing
the test to fail. Skip the test when CI=true or GITHUB_ACTIONS=true.

cmd/bd/doctor/fix/common.go

@@ -8,8 +8,13 @@ import (
 	"strings"
 )
 
+// ErrTestBinary is returned when getBdBinary detects it's running as a test binary.
+// This prevents fork bombs when tests call functions that execute bd subcommands.
+var ErrTestBinary = fmt.Errorf("running as test binary - cannot execute bd subcommands")
+
 // getBdBinary returns the path to the bd binary to use for fix operations.
 // It prefers the current executable to avoid command injection attacks.
+// Returns ErrTestBinary if running as a test binary to prevent fork bombs.
 func getBdBinary() (string, error) {
 	// Prefer current executable for security
 	exe, err := os.Executable()
@@ -17,8 +22,16 @@ func getBdBinary() (string, error) {
 		// Resolve symlinks to get the real binary path
 		realPath, err := filepath.EvalSymlinks(exe)
 		if err == nil {
-			return realPath, nil
+			exe = realPath
 		}
+
+		// Check if we're running as a test binary - this prevents fork bombs
+		// when tests call functions that execute bd subcommands
+		baseName := filepath.Base(exe)
+		if strings.HasSuffix(baseName, ".test") || strings.Contains(baseName, ".test.") {
+			return "", ErrTestBinary
+		}
+
 		return exe, nil
 	}