feat(state): Preserve selected project roots

cmd/context_evidence_test.go

@@ -12,6 +12,7 @@ import (
 	"time"
 
 	"codemap/analysis"
+	"codemap/internal/projectpath"
 	"codemap/scanner"
 	"codemap/watch"
 )
@@ -252,7 +253,7 @@ func TestHookPromptSubmitDoesNotClaimRiskFromCachedGraph(t *testing.T) {
 		}
 	})
 
-	status, err := os.ReadFile(filepath.Join(root, ".codemap", "status"))
+	status, err := os.ReadFile(filepath.Join(projectpath.ProjectRuntimeDir(root), "status"))
 	if err != nil {
 		t.Fatal(err)
 	}

cmd/context_test.go

@@ -8,6 +8,7 @@ import (
 	"testing"
 	"time"
 
+	"codemap/internal/projectpath"
 	"codemap/watch"
 )
 
@@ -92,7 +93,7 @@ func TestBuildContextEnvelopeFallsBackToConfiguredScanForLegacyState(t *testing.
 	if err != nil {
 		t.Fatal(err)
 	}
-	mustWriteFile(t, filepath.Join(root, ".codemap", "state.json"), string(legacyState))
+	mustWriteFile(t, filepath.Join(projectpath.ProjectRuntimeDir(root), "state.json"), string(legacyState))
 
 	envelope := buildContextEnvelope(root, "", true)
 

cmd/hooks.go

@@ -539,7 +539,7 @@ func showLightweightDiffVsMain(root string) {
 
 // getLastSessionEvents reads events.log for previous session context
 func getLastSessionEvents(root string) []string {
-	eventsFile := filepath.Join(projectpath.RuntimeCodemapDir(root), "events.log")
+	eventsFile := filepath.Join(projectpath.ProjectRuntimeDir(root), "events.log")
 	f, err := os.Open(eventsFile)
 	if err != nil {
 		return nil
@@ -887,7 +887,7 @@ func hookPromptSubmit(root string) error {
 
 // writeStatuslineState writes a tiny file for the statusline to read.
 func writeStatuslineState(root string, intent TaskIntent) {
-	codemapDir := projectpath.RuntimeCodemapDir(root)
+	codemapDir := projectpath.ProjectRuntimeDir(root)
 	status := intent.Category
 	if intent.RiskLevel != "low" {
 		status += " " + intent.RiskLevel
@@ -1379,7 +1379,7 @@ func showSessionProgress(root, sessionID string) {
 
 // hookPreCompact saves hub state before context compaction
 func hookPreCompact(root string) error {
-	codemapDir := projectpath.RuntimeCodemapDir(root)
+	codemapDir := projectpath.ProjectRuntimeDir(root)
 	if err := os.MkdirAll(codemapDir, 0755); err != nil {
 		return err
 	}
@@ -1694,7 +1694,7 @@ func updateSessionLease(root, sessionID string, active bool, now time.Time, acti
 		}
 		return nil
 	}
-	codemapDir := projectpath.RuntimeCodemapDir(root)
+	codemapDir := projectpath.ProjectRuntimeDir(root)
 	if err := os.MkdirAll(codemapDir, 0o755); err != nil {
 		return err
 	}

cmd/hooks_more_test.go

@@ -129,7 +129,7 @@ func mustJSONInput(t *testing.T, v any) string {
 func writeProjectConfig(t *testing.T, root string, cfg config.ProjectConfig) {
 	t.Helper()
 
-	if err := os.MkdirAll(filepath.Join(root, ".codemap"), 0o755); err != nil {
+	if err := os.MkdirAll(projectpath.ProjectRuntimeDir(root), 0o755); err != nil {
 		t.Fatal(err)
 	}
 	data, err := json.Marshal(cfg)
@@ -144,14 +144,14 @@ func writeProjectConfig(t *testing.T, root string, cfg config.ProjectConfig) {
 func writeStateOnly(t *testing.T, root string, state watch.State) {
 	t.Helper()
 
-	if err := os.MkdirAll(filepath.Join(root, ".codemap"), 0o755); err != nil {
+	if err := os.MkdirAll(projectpath.ProjectRuntimeDir(root), 0o755); err != nil {
 		t.Fatal(err)
 	}
 	data, err := json.Marshal(state)
 	if err != nil {
 		t.Fatal(err)
 	}
-	if err := os.WriteFile(filepath.Join(root, ".codemap", "state.json"), data, 0o644); err != nil {
+	if err := os.WriteFile(filepath.Join(projectpath.ProjectRuntimeDir(root), "state.json"), data, 0o644); err != nil {
 		t.Fatal(err)
 	}
 }
@@ -180,12 +180,12 @@ func TestWaitForDaemonState(t *testing.T) {
 	go func() {
 		defer close(done)
 		time.Sleep(150 * time.Millisecond)
-		_ = os.MkdirAll(filepath.Join(root, ".codemap"), 0o755)
+		_ = os.MkdirAll(projectpath.ProjectRuntimeDir(root), 0o755)
 		data, _ := json.Marshal(watch.State{
 			UpdatedAt: time.Now(),
 			FileCount: 7,
 		})
-		_ = os.WriteFile(filepath.Join(root, ".codemap", "state.json"), data, 0o644)
+		_ = os.WriteFile(filepath.Join(projectpath.ProjectRuntimeDir(root), "state.json"), data, 0o644)
 	}()
 
 	state := waitForDaemonState(root, time.Second)
@@ -890,7 +890,7 @@ func TestHookFilesUseSetupRoot(t *testing.T) {
 	setupRoot := t.TempDir()
 	projectpath.SetSetupRoot(setupRoot)
 	t.Cleanup(projectpath.ResetSetupRoot)
-	codemapDir := filepath.Join(setupRoot, ".codemap")
+	codemapDir := projectpath.ProjectRuntimeDir(projectRoot)
 	if err := os.MkdirAll(codemapDir, 0o755); err != nil {
 		t.Fatal(err)
 	}
@@ -921,23 +921,29 @@ func TestAutomaticLinkedWorktreeUsesLocalHookState(t *testing.T) {
 	if err := os.MkdirAll(gitDir, 0o755); err != nil {
 		t.Fatal(err)
 	}
-	if err := os.MkdirAll(filepath.Join(primary, ".codemap"), 0o755); err != nil {
+	if err := os.MkdirAll(projectpath.ProjectRuntimeDir(primary), 0o755); err != nil {
 		t.Fatal(err)
 	}
-	if err := os.WriteFile(filepath.Join(primary, ".codemap", "events.log"), []byte("primary event\n"), 0o644); err != nil {
+	if err := os.MkdirAll(projectpath.ProjectRuntimeDir(primary), 0o755); err != nil {
+		t.Fatal(err)
+	}
+	if err := os.WriteFile(filepath.Join(projectpath.ProjectRuntimeDir(primary), "events.log"), []byte("primary event\n"), 0o644); err != nil {
 		t.Fatal(err)
 	}
 	if err := os.WriteFile(filepath.Join(gitDir, "commondir"), []byte("../..\n"), 0o644); err != nil {
 		t.Fatal(err)
 	}
 	linked := filepath.Join(t.TempDir(), "linked")
-	if err := os.MkdirAll(filepath.Join(linked, ".codemap"), 0o755); err != nil {
+	if err := os.MkdirAll(projectpath.ProjectRuntimeDir(linked), 0o755); err != nil {
 		t.Fatal(err)
 	}
 	if err := os.WriteFile(filepath.Join(linked, ".git"), []byte("gitdir: "+gitDir+"\n"), 0o644); err != nil {
 		t.Fatal(err)
 	}
-	if err := os.WriteFile(filepath.Join(linked, ".codemap", "events.log"), []byte("linked event\n"), 0o644); err != nil {
+	if err := os.MkdirAll(projectpath.ProjectRuntimeDir(linked), 0o755); err != nil {
+		t.Fatal(err)
+	}
+	if err := os.WriteFile(filepath.Join(projectpath.ProjectRuntimeDir(linked), "events.log"), []byte("linked event\n"), 0o644); err != nil {
 		t.Fatal(err)
 	}
 	linked, _ = filepath.EvalSymlinks(linked)
@@ -947,7 +953,7 @@ func TestAutomaticLinkedWorktreeUsesLocalHookState(t *testing.T) {
 		t.Fatalf("getLastSessionEvents() = %#v, want linked event", events)
 	}
 	writeStatuslineState(linked, TaskIntent{Category: "feature", RiskLevel: "low"})
-	if _, err := os.Stat(filepath.Join(linked, ".codemap", "status")); err != nil {
+	if _, err := os.Stat(filepath.Join(projectpath.ProjectRuntimeDir(linked), "status")); err != nil {
 		t.Fatalf("linked status missing: %v", err)
 	}
 	if _, err := os.Stat(filepath.Join(primary, ".codemap", "status")); !os.IsNotExist(err) {
@@ -956,7 +962,7 @@ func TestAutomaticLinkedWorktreeUsesLocalHookState(t *testing.T) {
 	if err := updateSessionLease(linked, "session-1", true, time.Now(), nil); err != nil {
 		t.Fatalf("updateSessionLease() error: %v", err)
 	}
-	entries, err := os.ReadDir(filepath.Join(linked, ".codemap", "sessions"))
+	entries, err := os.ReadDir(filepath.Join(projectpath.ProjectRuntimeDir(linked), "sessions"))
 	if err != nil || len(entries) != 1 {
 		t.Fatalf("linked session lease entries = %d, err = %v", len(entries), err)
 	}

cmd/hooks_provenance_test.go

@@ -8,6 +8,7 @@ import (
 	"testing"
 	"time"
 
+	"codemap/internal/projectpath"
 	"codemap/watch"
 )
 
@@ -29,10 +30,10 @@ func writeProvenanceState(t *testing.T, root string, paths []string) {
 	if err != nil {
 		t.Fatal(err)
 	}
-	if err := os.MkdirAll(filepath.Join(root, ".codemap"), 0o755); err != nil {
+	if err := os.MkdirAll(projectpath.ProjectRuntimeDir(root), 0o755); err != nil {
 		t.Fatal(err)
 	}
-	if err := os.WriteFile(filepath.Join(root, ".codemap", "state.json"), data, 0o644); err != nil {
+	if err := os.WriteFile(filepath.Join(projectpath.ProjectRuntimeDir(root), "state.json"), data, 0o644); err != nil {
 		t.Fatal(err)
 	}
 }

cmd/hooks_test.go

@@ -13,6 +13,7 @@ import (
 
 	"codemap/config"
 	"codemap/handoff"
+	"codemap/internal/projectpath"
 	"codemap/limits"
 	"codemap/watch"
 )
@@ -243,7 +244,7 @@ func TestShouldRestartDaemon(t *testing.T) {
 	t.Run("running without state returns true", func(t *testing.T) {
 		withOwnedDaemonProcess(t, func(string) bool { return true })
 		root := t.TempDir()
-		codemapDir := filepath.Join(root, ".codemap")
+		codemapDir := projectpath.ProjectRuntimeDir(root)
 		if err := os.MkdirAll(codemapDir, 0755); err != nil {
 			t.Fatal(err)
 		}
@@ -802,7 +803,7 @@ func captureOutput(f func()) string {
 // and a PID file pointing to the current process so IsRunning returns true.
 func writeWatchState(t *testing.T, root string, state watch.State) {
 	t.Helper()
-	codemapDir := filepath.Join(root, ".codemap")
+	codemapDir := projectpath.ProjectRuntimeDir(root)
 	if err := os.MkdirAll(codemapDir, 0755); err != nil {
 		t.Fatal(err)
 	}
@@ -830,7 +831,7 @@ func TestGetLastSessionEvents(t *testing.T) {
 
 	t.Run("empty file returns nil", func(t *testing.T) {
 		root := t.TempDir()
-		codemapDir := filepath.Join(root, ".codemap")
+		codemapDir := projectpath.ProjectRuntimeDir(root)
 		if err := os.MkdirAll(codemapDir, 0755); err != nil {
 			t.Fatal(err)
 		}
@@ -844,7 +845,7 @@ func TestGetLastSessionEvents(t *testing.T) {
 
 	t.Run("returns all lines when fewer than 20", func(t *testing.T) {
 		root := t.TempDir()
-		codemapDir := filepath.Join(root, ".codemap")
+		codemapDir := projectpath.ProjectRuntimeDir(root)
 		os.MkdirAll(codemapDir, 0755)
 		lines := "ts|WRITE|a.go\nts|WRITE|b.go\nts|WRITE|c.go"
 		os.WriteFile(filepath.Join(codemapDir, "events.log"), []byte(lines), 0644)
@@ -857,7 +858,7 @@ func TestGetLastSessionEvents(t *testing.T) {
 
 	t.Run("caps at 20 lines for large log (context bloat protection)", func(t *testing.T) {
 		root := t.TempDir()
-		codemapDir := filepath.Join(root, ".codemap")
+		codemapDir := projectpath.ProjectRuntimeDir(root)
 		os.MkdirAll(codemapDir, 0755)
 
 		var sb strings.Builder
@@ -881,7 +882,7 @@ func TestGetLastSessionEvents(t *testing.T) {
 
 	t.Run("reads only tail of huge event log and still returns latest 20", func(t *testing.T) {
 		root := t.TempDir()
-		codemapDir := filepath.Join(root, ".codemap")
+		codemapDir := projectpath.ProjectRuntimeDir(root)
 		os.MkdirAll(codemapDir, 0755)
 
 		var sb strings.Builder
@@ -904,7 +905,7 @@ func TestGetLastSessionEvents(t *testing.T) {
 
 	t.Run("skips blank lines when counting", func(t *testing.T) {
 		root := t.TempDir()
-		codemapDir := filepath.Join(root, ".codemap")
+		codemapDir := projectpath.ProjectRuntimeDir(root)
 		os.MkdirAll(codemapDir, 0755)
 		// 5 real entries surrounded by blank lines
 		content := "\nts|WRITE|a.go\n\nts|WRITE|b.go\n\n\nts|WRITE|c.go\n\nts|WRITE|d.go\nts|WRITE|e.go\n"
@@ -1141,7 +1142,7 @@ func TestHookPreCompact(t *testing.T) {
 		if out != "" {
 			t.Errorf("expected no output when no hubs, got %q", out)
 		}
-		hubsFile := filepath.Join(root, ".codemap", "hubs.txt")
+		hubsFile := filepath.Join(projectpath.ProjectRuntimeDir(root), "hubs.txt")
 		if _, err := os.Stat(hubsFile); !os.IsNotExist(err) {
 			t.Error("expected no hubs.txt when hub list is empty")
 		}
@@ -1173,7 +1174,7 @@ func TestHookPreCompact(t *testing.T) {
 			t.Errorf("expected hubs.txt mention, got %q", out)
 		}
 
-		hubsFile := filepath.Join(root, ".codemap", "hubs.txt")
+		hubsFile := filepath.Join(projectpath.ProjectRuntimeDir(root), "hubs.txt")
 		content, err := os.ReadFile(hubsFile)
 		if err != nil {
 			t.Fatalf("expected hubs.txt to be created: %v", err)

cmd/setup_review_test.go

@@ -6,6 +6,8 @@ import (
 	"strings"
 	"testing"
 	"time"
+
+	"codemap/internal/projectpath"
 )
 
 func TestEnsureClaudeMCPPreservesLargeIntegersAndUnknownKeys(t *testing.T) {
@@ -219,7 +221,7 @@ func TestUpdateSessionLeaseTracksActiveSessionsAndPrunesStale(t *testing.T) {
 	}
 
 	// Age session-b's lease past the TTL; the next update must reclaim it.
-	leaseDir := filepath.Join(root, ".codemap", "sessions")
+	leaseDir := filepath.Join(projectpath.ProjectRuntimeDir(root), "sessions")
 	entries, err := os.ReadDir(leaseDir)
 	if err != nil {
 		t.Fatal(err)
@@ -247,7 +249,7 @@ func TestUpdateSessionLeaseTracksActiveSessionsAndPrunesStale(t *testing.T) {
 
 func TestUpdateSessionLeaseReclaimsStaleLock(t *testing.T) {
 	root := t.TempDir()
-	lockPath := filepath.Join(root, ".codemap", "sessions.lock")
+	lockPath := filepath.Join(projectpath.ProjectRuntimeDir(root), "sessions.lock")
 	if err := os.MkdirAll(lockPath, 0o700); err != nil {
 		t.Fatal(err)
 	}

handoff/handoff_test.go

@@ -9,6 +9,7 @@ import (
 	"testing"
 	"time"
 
+	"codemap/internal/projectpath"
 	"codemap/watch"
 )
 
@@ -331,3 +332,54 @@ func TestMetricsLogCapped(t *testing.T) {
 		t.Fatalf("expected %d metrics lines after cap, got %d", maxMetricsLines, len(lines))
 	}
 }
+
+func TestStoragePathsUseSetupRoot(t *testing.T) {
+	projectRoot := t.TempDir()
+	setupRoot := t.TempDir()
+	projectpath.SetSetupRoot(setupRoot)
+	t.Cleanup(projectpath.ResetSetupRoot)
+
+	want := filepath.Join(projectpath.ProjectRuntimeDir(projectRoot), latestFilename)
+	if got := LatestPath(projectRoot); got != want {
+		t.Fatalf("LatestPath() = %q, want %q", got, want)
+	}
+}
+
+func TestAutomaticLinkedWorktreesUseDistinctHandoffStorage(t *testing.T) {
+	projectpath.ResetSetupRoot()
+	t.Cleanup(projectpath.ResetSetupRoot)
+	primary := t.TempDir()
+	if err := os.MkdirAll(filepath.Join(primary, ".codemap"), 0o755); err != nil {
+		t.Fatal(err)
+	}
+	makeLinked := func(name string) string {
+		gitDir := filepath.Join(primary, ".git", "worktrees", name)
+		if err := os.MkdirAll(gitDir, 0o755); err != nil {
+			t.Fatal(err)
+		}
+		if err := os.WriteFile(filepath.Join(gitDir, "commondir"), []byte("../..\n"), 0o644); err != nil {
+			t.Fatal(err)
+		}
+		linked := filepath.Join(t.TempDir(), name)
+		if err := os.MkdirAll(linked, 0o755); err != nil {
+			t.Fatal(err)
+		}
+		if err := os.WriteFile(filepath.Join(linked, ".git"), []byte("gitdir: "+gitDir+"\n"), 0o644); err != nil {
+			t.Fatal(err)
+		}
+		linked, _ = filepath.EvalSymlinks(linked)
+		return linked
+	}
+	linkedA := makeLinked("a")
+	linkedB := makeLinked("b")
+
+	if got, want := LatestPath(linkedA), filepath.Join(projectpath.ProjectRuntimeDir(linkedA), latestFilename); got != want {
+		t.Fatalf("LatestPath(A) = %q, want %q", got, want)
+	}
+	if got, want := LatestPath(linkedB), filepath.Join(projectpath.ProjectRuntimeDir(linkedB), latestFilename); got != want {
+		t.Fatalf("LatestPath(B) = %q, want %q", got, want)
+	}
+	if LatestPath(linkedA) == LatestPath(linkedB) {
+		t.Fatal("automatic linked worktrees unexpectedly share handoff storage")
+	}
+}