diff --git a/cmd/entire/cli/paths/paths.go b/cmd/entire/cli/paths/paths.go
index f22617249..09d6f423c 100644
--- a/cmd/entire/cli/paths/paths.go
+++ b/cmd/entire/cli/paths/paths.go
@@ -152,20 +152,6 @@ func IsSubpath(parent, child string) bool {
 	return rel != ".." && !strings.HasPrefix(rel, ".."+string(filepath.Separator))
 }
 
-// ToRelativePath converts an absolute path to relative.
-// Returns empty string if the path is outside the working directory.
-func ToRelativePath(absPath, cwd string) string {
-	if !filepath.IsAbs(absPath) {
-		return absPath
-	}
-	relPath, err := filepath.Rel(cwd, absPath)
-	if err != nil || strings.HasPrefix(relPath, "..") {
-		return ""
-	}
-
-	return relPath
-}
-
 // nonAlphanumericRegex matches any non-alphanumeric character
 var nonAlphanumericRegex = regexp.MustCompile(`[^a-zA-Z0-9]`)
 
diff --git a/cmd/entire/cli/paths/relative_unix.go b/cmd/entire/cli/paths/relative_unix.go
new file mode 100644
index 000000000..4be38ddf5
--- /dev/null
+++ b/cmd/entire/cli/paths/relative_unix.go
@@ -0,0 +1,22 @@
+//go:build unix
+
+package paths
+
+import (
+	"path/filepath"
+	"strings"
+)
+
+// ToRelativePath converts an absolute path to relative.
+// Returns empty string if the path is outside the working directory.
+func ToRelativePath(absPath, cwd string) string {
+	if !filepath.IsAbs(absPath) {
+		return absPath
+	}
+	relPath, err := filepath.Rel(cwd, absPath)
+	if err != nil || strings.HasPrefix(relPath, "..") {
+		return ""
+	}
+
+	return relPath
+}
diff --git a/cmd/entire/cli/paths/relative_unix_test.go b/cmd/entire/cli/paths/relative_unix_test.go
new file mode 100644
index 000000000..0eaacd13c
--- /dev/null
+++ b/cmd/entire/cli/paths/relative_unix_test.go
@@ -0,0 +1,39 @@
+//go:build unix
+
+package paths
+
+import (
+	"testing"
+)
+
+func TestToRelativePath(t *testing.T) {
+	t.Parallel()
+	tests := []struct {
+		name    string
+		absPath string
+		cwd     string
+		want    string
+	}{
+		// Standard relative conversion
+		{name: "child of cwd", absPath: "/repo/docs/red.md", cwd: "/repo", want: "docs/red.md"},
+		{name: "exact cwd", absPath: "/repo", cwd: "/repo", want: "."},
+		{name: "outside cwd", absPath: "/other/file.txt", cwd: "/repo", want: ""},
+
+		// Already relative — pass through
+		{name: "relative unchanged", absPath: "docs/red.md", cwd: "/repo", want: "docs/red.md"},
+
+		// Unix paths that are valid on this platform
+		{name: "tmp is valid unix path", absPath: "/tmp/repo/file.txt", cwd: "/tmp/repo", want: "file.txt"},
+		{name: "home is valid unix path", absPath: "/home/user/repo/f.go", cwd: "/home/user/repo", want: "f.go"},
+		{name: "slash-c is valid unix path", absPath: "/c/Users/repo/f.go", cwd: "/c/Users/repo", want: "f.go"},
+	}
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			t.Parallel()
+			got := ToRelativePath(tt.absPath, tt.cwd)
+			if got != tt.want {
+				t.Errorf("ToRelativePath(%q, %q) = %q, want %q", tt.absPath, tt.cwd, got, tt.want)
+			}
+		})
+	}
+}
diff --git a/cmd/entire/cli/paths/relative_windows.go b/cmd/entire/cli/paths/relative_windows.go
new file mode 100644
index 000000000..b89b7918b
--- /dev/null
+++ b/cmd/entire/cli/paths/relative_windows.go
@@ -0,0 +1,62 @@
+//go:build windows
+
+package paths
+
+import (
+	"os"
+	"path/filepath"
+	"regexp"
+	"strings"
+)
+
+// msysDrivePrefix matches MSYS/Git-Bash-style absolute paths like /c/ or /D/.
+// Git for Windows executes hooks through MSYS2 bash, which converts Windows paths
+// (C:\Users\...) to Unix-style (/c/Users/...) in tool output and transcripts.
+var msysDrivePrefix = regexp.MustCompile(`^/([a-zA-Z])/`)
+
+// NormalizeMSYSPath converts MSYS/Git-Bash paths to Windows paths.
+// Handles two MSYS conventions:
+//   - Drive paths: /c/Users/... → C:/Users/...
+//   - Virtual dirs: /tmp/... → <TEMP>/... (MSYS2 maps /tmp to the Windows temp dir)
+//
+// Returns the input unchanged if the path doesn't match any known MSYS pattern.
+func NormalizeMSYSPath(p string) string {
+	if m := msysDrivePrefix.FindStringSubmatch(p); m != nil {
+		return strings.ToUpper(m[1]) + ":/" + p[3:]
+	}
+	// MSYS2 maps /tmp to the Windows temp directory.
+	if strings.HasPrefix(p, "/tmp/") {
+		if tmp := os.TempDir(); tmp != "" {
+			return filepath.Join(tmp, p[5:])
+		}
+	}
+	return p
+}
+
+// ToRelativePath converts an absolute path to relative.
+// Returns empty string if the path is outside the working directory.
+//
+// On Windows, transcript-extracted paths may arrive in Unix formats from
+// MSYS2/Git Bash (/c/Users/..., /tmp/...) or agent sandboxes (/home/user/...).
+// These are normalized via NormalizeMSYSPath, and any remaining Unix-style
+// paths that the OS can't resolve are dropped.
+func ToRelativePath(absPath, cwd string) string {
+	absPath = NormalizeMSYSPath(absPath)
+
+	// After MSYS normalization, a path starting with "/" that the OS still
+	// doesn't recognize as absolute is an unconvertible Unix path (e.g.,
+	// /home/user/... from a container/sandbox). Filter it out.
+	if strings.HasPrefix(absPath, "/") && !filepath.IsAbs(absPath) {
+		return ""
+	}
+
+	if !filepath.IsAbs(absPath) {
+		return absPath
+	}
+	relPath, err := filepath.Rel(cwd, absPath)
+	if err != nil || strings.HasPrefix(relPath, "..") {
+		return ""
+	}
+
+	return relPath
+}
diff --git a/cmd/entire/cli/paths/relative_windows_test.go b/cmd/entire/cli/paths/relative_windows_test.go
new file mode 100644
index 000000000..e737338c6
--- /dev/null
+++ b/cmd/entire/cli/paths/relative_windows_test.go
@@ -0,0 +1,78 @@
+//go:build windows
+
+package paths
+
+import (
+	"os"
+	"path/filepath"
+	"testing"
+)
+
+func TestNormalizeMSYSPath(t *testing.T) {
+	t.Parallel()
+	tests := []struct {
+		name string
+		in   string
+		want string
+	}{
+		// Drive letter paths
+		{name: "lowercase drive", in: "/c/Users/Victor/repo", want: "C:/Users/Victor/repo"},
+		{name: "uppercase drive", in: "/D/Projects/app", want: "D:/Projects/app"},
+		{name: "drive root", in: "/c/", want: "C:/"},
+
+		// /tmp mapping
+		{name: "tmp path", in: "/tmp/e2e-repo-123/docs/red.md", want: filepath.Join(os.TempDir(), "e2e-repo-123", "docs", "red.md")},
+		{name: "tmp root file", in: "/tmp/file.txt", want: filepath.Join(os.TempDir(), "file.txt")},
+
+		// Paths that should NOT be converted
+		{name: "already relative", in: "docs/red.md", want: "docs/red.md"},
+		{name: "windows absolute", in: "C:/Users/Victor/repo", want: "C:/Users/Victor/repo"},
+		{name: "unix absolute non-drive", in: "/home/user/docs/red.md", want: "/home/user/docs/red.md"},
+		{name: "empty string", in: "", want: ""},
+		{name: "single slash", in: "/", want: "/"},
+		{name: "tmp exact no trailing slash", in: "/tmp", want: "/tmp"},
+	}
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			t.Parallel()
+			got := NormalizeMSYSPath(tt.in)
+			if got != tt.want {
+				t.Errorf("NormalizeMSYSPath(%q) = %q, want %q", tt.in, got, tt.want)
+			}
+		})
+	}
+}
+
+func TestToRelativePath(t *testing.T) {
+	t.Parallel()
+	tests := []struct {
+		name    string
+		absPath string
+		cwd     string
+		want    string
+	}{
+		// Standard relative conversion
+		{name: "child of cwd", absPath: "C:/repo/docs/red.md", cwd: "C:/repo", want: "docs/red.md"},
+		{name: "exact cwd", absPath: "C:/repo", cwd: "C:/repo", want: "."},
+		{name: "outside cwd", absPath: "C:/other/file.txt", cwd: "C:/repo", want: ""},
+
+		// Already relative — pass through
+		{name: "relative unchanged", absPath: "docs/red.md", cwd: "C:/repo", want: "docs/red.md"},
+
+		// MSYS drive paths get normalized and resolved
+		{name: "msys drive path", absPath: "/c/repo/docs/red.md", cwd: "C:/repo", want: "docs/red.md"},
+
+		// Container/sandbox paths are dropped (can't resolve on Windows)
+		{name: "container path dropped", absPath: "/home/user/docs/red.md", cwd: "C:/repo", want: ""},
+		{name: "unix opt path dropped", absPath: "/opt/app/file.txt", cwd: "C:/repo", want: ""},
+	}
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			t.Parallel()
+			got := ToRelativePath(tt.absPath, tt.cwd)
+			if got != tt.want {
+				t.Errorf("ToRelativePath(%q, %q) = %q, want %q", tt.absPath, tt.cwd, got, tt.want)
+			}
+		})
+	}
+}
diff --git a/cmd/entire/cli/state.go b/cmd/entire/cli/state.go
index 545f6e0b6..0d7e684eb 100644
--- a/cmd/entire/cli/state.go
+++ b/cmd/entire/cli/state.go
@@ -297,21 +297,37 @@ func filterToUncommittedFiles(ctx context.Context, files []string, repoRoot stri
 
 	repo, err := openRepository(ctx)
 	if err != nil {
+		logging.Warn(ctx, "filterToUncommittedFiles: failed to open repository, keeping all files",
+			slog.String("error", err.Error()),
+			slog.String("dir", repoRoot),
+			slog.Any("files", files))
 		return files // fail open
 	}
 
 	head, err := repo.Head()
 	if err != nil {
+		logging.Warn(ctx, "filterToUncommittedFiles: failed to resolve HEAD, keeping all files",
+			slog.String("error", err.Error()),
+			slog.String("dir", repoRoot),
+			slog.Any("files", files))
 		return files // fail open (empty repo, detached HEAD, etc.)
 	}
 
 	commit, err := repo.CommitObject(head.Hash())
 	if err != nil {
+		logging.Warn(ctx, "filterToUncommittedFiles: failed to get commit object, keeping all files",
+			slog.String("error", err.Error()),
+			slog.String("dir", repoRoot),
+			slog.Any("files", files))
 		return files // fail open
 	}
 
 	headTree, err := commit.Tree()
 	if err != nil {
+		logging.Warn(ctx, "filterToUncommittedFiles: failed to get commit tree, keeping all files",
+			slog.String("error", err.Error()),
+			slog.String("dir", repoRoot),
+			slog.Any("files", files))
 		return files // fail open
 	}