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.

internal/syncbranch/worktree_path_test.go

@@ -107,6 +107,13 @@ func TestGetBeadsWorktreePath(t *testing.T) {
 		// Should point to the main repo's .git/beads-worktrees, not the worktree's
 		mainGitDir := filepath.Join(mainRepoPath, ".git")
 		expectedPath := filepath.Join(mainGitDir, "beads-worktrees", "beads-sync")
+
+		// Resolve symlinks for comparison (on macOS, /var -> /private/var)
+		resolvedExpected, err := filepath.EvalSymlinks(mainRepoPath)
+		if err == nil {
+			expectedPath = filepath.Join(resolvedExpected, ".git", "beads-worktrees", "beads-sync")
+		}
+
 		if path != expectedPath {
 			t.Errorf("Expected path %q, got %q", expectedPath, path)
 		}

internal/ui/styles.go

@@ -0,0 +1,130 @@
+// Package ui provides terminal styling for beads CLI output.
+// Uses the Ayu color theme with adaptive light/dark mode support.
+package ui
+
+import (
+	"strings"
+
+	"github.com/charmbracelet/lipgloss"
+)
+
+// Ayu theme color palette
+// Dark: https://terminalcolors.com/themes/ayu/dark/
+// Light: https://terminalcolors.com/themes/ayu/light/
+var (
+	// Semantic status colors (Ayu theme - adaptive light/dark)
+	ColorPass = lipgloss.AdaptiveColor{
+		Light: "#86b300", // ayu light bright green
+		Dark:  "#c2d94c", // ayu dark bright green
+	}
+	ColorWarn = lipgloss.AdaptiveColor{
+		Light: "#f2ae49", // ayu light bright yellow
+		Dark:  "#ffb454", // ayu dark bright yellow
+	}
+	ColorFail = lipgloss.AdaptiveColor{
+		Light: "#f07171", // ayu light bright red
+		Dark:  "#f07178", // ayu dark bright red
+	}
+	ColorMuted = lipgloss.AdaptiveColor{
+		Light: "#828c99", // ayu light muted
+		Dark:  "#6c7680", // ayu dark muted
+	}
+	ColorAccent = lipgloss.AdaptiveColor{
+		Light: "#399ee6", // ayu light bright blue
+		Dark:  "#59c2ff", // ayu dark bright blue
+	}
+)
+
+// Status styles - consistent across all commands
+var (
+	PassStyle   = lipgloss.NewStyle().Foreground(ColorPass)
+	WarnStyle   = lipgloss.NewStyle().Foreground(ColorWarn)
+	FailStyle   = lipgloss.NewStyle().Foreground(ColorFail)
+	MutedStyle  = lipgloss.NewStyle().Foreground(ColorMuted)
+	AccentStyle = lipgloss.NewStyle().Foreground(ColorAccent)
+)
+
+// CategoryStyle for section headers - bold with accent color
+var CategoryStyle = lipgloss.NewStyle().Bold(true).Foreground(ColorAccent)
+
+// Status icons - consistent semantic indicators
+const (
+	IconPass = "✓"
+	IconWarn = "⚠"
+	IconFail = "✗"
+	IconSkip = "-"
+	IconInfo = "ℹ"
+)
+
+// Tree characters for hierarchical display
+const (
+	TreeChild  = "⎿ "  // child indicator
+	TreeLast   = "└─ " // last child / detail line
+	TreeIndent = "  "  // 2-space indent per level
+)
+
+// Separators
+const (
+	SeparatorLight = "──────────────────────────────────────────"
+	SeparatorHeavy = "══════════════════════════════════════════"
+)
+
+// RenderPass renders text with pass (green) styling
+func RenderPass(s string) string {
+	return PassStyle.Render(s)
+}
+
+// RenderWarn renders text with warning (yellow) styling
+func RenderWarn(s string) string {
+	return WarnStyle.Render(s)
+}
+
+// RenderFail renders text with fail (red) styling
+func RenderFail(s string) string {
+	return FailStyle.Render(s)
+}
+
+// RenderMuted renders text with muted (gray) styling
+func RenderMuted(s string) string {
+	return MutedStyle.Render(s)
+}
+
+// RenderAccent renders text with accent (blue) styling
+func RenderAccent(s string) string {
+	return AccentStyle.Render(s)
+}
+
+// RenderCategory renders a category header in uppercase with accent color
+func RenderCategory(s string) string {
+	return CategoryStyle.Render(strings.ToUpper(s))
+}
+
+// RenderSeparator renders the light separator line in muted color
+func RenderSeparator() string {
+	return MutedStyle.Render(SeparatorLight)
+}
+
+// RenderPassIcon renders the pass icon with styling
+func RenderPassIcon() string {
+	return PassStyle.Render(IconPass)
+}
+
+// RenderWarnIcon renders the warning icon with styling
+func RenderWarnIcon() string {
+	return WarnStyle.Render(IconWarn)
+}
+
+// RenderFailIcon renders the fail icon with styling
+func RenderFailIcon() string {
+	return FailStyle.Render(IconFail)
+}
+
+// RenderSkipIcon renders the skip icon with styling
+func RenderSkipIcon() string {
+	return MutedStyle.Render(IconSkip)
+}
+
+// RenderInfoIcon renders the info icon with styling
+func RenderInfoIcon() string {
+	return AccentStyle.Render(IconInfo)
+}