fix: skip empty .git directories during repo discovery

src/daemon/analyzers/history.rs

@@ -773,6 +773,7 @@ mod tests {
         let worktree = dir.path();
         let git_dir = worktree.join(".git");
         fs::create_dir_all(git_dir.join("logs")).expect("create logs");
+        fs::write(git_dir.join("HEAD"), "ref: refs/heads/main\n").expect("write HEAD");
         fs::write(
             git_dir.join("logs").join("HEAD"),
             concat!(

src/daemon/trace_normalizer.rs

@@ -1810,6 +1810,7 @@ mod tests {
         let temp = tempfile::tempdir().expect("create tempdir");
         let worktree = temp.path().join("repo");
         fs::create_dir_all(worktree.join(".git")).expect("create git dir");
+        fs::write(worktree.join(".git/HEAD"), "ref: refs/heads/main\n").expect("write HEAD");
         backend.set_alias(worktree.to_str().expect("utf8 worktree"), "ci", "commit");
         let mut normalizer = TraceNormalizer::new(backend);
 
@@ -2015,6 +2016,7 @@ mod tests {
         let outer = temp.path().join("outer");
         let clone_dir = outer.join("nested").join("relative-clone");
         fs::create_dir_all(clone_dir.join(".git")).expect("create clone git dir");
+        fs::write(clone_dir.join(".git/HEAD"), "ref: refs/heads/main\n").expect("write HEAD");
 
         let start = serde_json::json!({
             "event":"start",
@@ -2086,6 +2088,7 @@ mod tests {
 
         // Simulate repo discoverability only once clone is about to exit.
         fs::create_dir_all(clone_dir.join(".git")).expect("create clone git dir");
+        fs::write(clone_dir.join(".git/HEAD"), "ref: refs/heads/main\n").expect("write HEAD");
 
         let cmd = normalizer
             .ingest_payload(&exit)
@@ -2104,7 +2107,9 @@ mod tests {
         let source_repo = temp.path().join("source-repo");
         let cloned_repo = temp.path().join("cloned-repo");
         fs::create_dir_all(source_repo.join(".git")).expect("create source git dir");
+        fs::write(source_repo.join(".git/HEAD"), "ref: refs/heads/main\n").expect("write HEAD");
         fs::create_dir_all(cloned_repo.join(".git")).expect("create cloned git dir");
+        fs::write(cloned_repo.join(".git/HEAD"), "ref: refs/heads/main\n").expect("write HEAD");
 
         let start = serde_json::json!({
             "event":"start",
@@ -2154,6 +2159,7 @@ mod tests {
         let cwd = temp.path().join("projects"); // non-repo CWD
         let clone_dest = cwd.join("testing-git"); // the clone destination
         fs::create_dir_all(clone_dest.join(".git")).expect("create clone git dir");
+        fs::write(clone_dest.join(".git/HEAD"), "ref: refs/heads/main\n").expect("write HEAD");
 
         let root_sid = "20260327T000000.000000Z-Hdeadbeef-P00010000";
         let child_sid = format!("{}/20260327T000000.000001Z-Hdeadbeef-P00010001", root_sid);
@@ -2244,7 +2250,9 @@ mod tests {
         let repo_a = temp.path().join("repo-a");
         let repo_b = temp.path().join("repo-b");
         fs::create_dir_all(repo_a.join(".git")).expect("create repo-a git dir");
+        fs::write(repo_a.join(".git/HEAD"), "ref: refs/heads/main\n").expect("write HEAD");
         fs::create_dir_all(repo_b.join(".git")).expect("create repo-b git dir");
+        fs::write(repo_b.join(".git/HEAD"), "ref: refs/heads/main\n").expect("write HEAD");
 
         let start_a = serde_json::json!({
             "event":"start",
@@ -2376,6 +2384,7 @@ mod tests {
         let temp = tempfile::tempdir().expect("create tempdir");
         let repo = temp.path().join("repo");
         fs::create_dir_all(repo.join(".git")).expect("create git dir");
+        fs::write(repo.join(".git/HEAD"), "ref: refs/heads/main\n").expect("write HEAD");
 
         let start = serde_json::json!({
             "event":"start",
@@ -2417,6 +2426,7 @@ mod tests {
         let temp = tempfile::tempdir().expect("create tempdir");
         let repo = temp.path().join("repo");
         fs::create_dir_all(repo.join(".git")).expect("create git dir");
+        fs::write(repo.join(".git/HEAD"), "ref: refs/heads/main\n").expect("write HEAD");
 
         let start = serde_json::json!({
             "event":"start",

src/git/repo_state.rs

@@ -13,11 +13,31 @@ pub struct HeadState {
     pub detached: bool,
 }
 
+/// Returns `true` if `dot_git` looks like a valid `.git` entry.
+///
+/// A `.git` *file* (worktree / submodule pointer) is always considered valid —
+/// its contents will be validated later when the pointer is resolved.
+///
+/// A `.git` *directory* is only valid when it contains a `HEAD` file, which is
+/// a fundamental invariant of every git repository (standard, bare, worktree,
+/// or submodule).  An empty `.git` directory (e.g. one accidentally created by
+/// docker-compose volume mounts) is rejected so that the tree-walk continues
+/// upward to the real repository.
+pub fn is_valid_git_dir(dot_git: &Path) -> bool {
+    if dot_git.is_file() {
+        return true;
+    }
+    if dot_git.is_dir() {
+        return dot_git.join("HEAD").is_file();
+    }
+    false
+}
+
 pub fn worktree_root_for_path(path: &Path) -> Option<PathBuf> {
     let mut current = Some(path);
     while let Some(candidate) = current {
         let dot_git = candidate.join(".git");
-        if dot_git.is_dir() || dot_git.is_file() {
+        if is_valid_git_dir(&dot_git) {
             return Some(candidate.to_path_buf());
         }
         current = candidate.parent();
@@ -673,6 +693,68 @@ mod tests {
         assert_eq!(resolved, worktree);
     }
 
+    #[test]
+    fn worktree_root_for_path_skips_empty_git_directory() {
+        let temp = tempfile::tempdir().unwrap();
+        let real_repo = temp.path();
+        // Real repo has a valid .git with HEAD
+        write_file(&real_repo.join(".git/HEAD"), "ref: refs/heads/main\n");
+
+        // Subdirectory with an empty .git (no HEAD) — should be skipped
+        let subdir = real_repo.join("services").join("app");
+        fs::create_dir_all(subdir.join(".git")).unwrap();
+
+        let nested = subdir.join("src");
+        fs::create_dir_all(&nested).unwrap();
+
+        let resolved = worktree_root_for_path(&nested).unwrap();
+        assert_eq!(resolved, real_repo.to_path_buf());
+    }
+
+    #[test]
+    fn worktree_root_for_path_finds_valid_git_directory() {
+        let temp = tempfile::tempdir().unwrap();
+        let repo = temp.path();
+        write_file(&repo.join(".git/HEAD"), "ref: refs/heads/main\n");
+
+        let nested = repo.join("src");
+        fs::create_dir_all(&nested).unwrap();
+
+        let resolved = worktree_root_for_path(&nested).unwrap();
+        assert_eq!(resolved, repo.to_path_buf());
+    }
+
+    #[test]
+    fn is_valid_git_dir_rejects_empty_directory() {
+        let temp = tempfile::tempdir().unwrap();
+        let dot_git = temp.path().join(".git");
+        fs::create_dir_all(&dot_git).unwrap();
+        assert!(!is_valid_git_dir(&dot_git));
+    }
+
+    #[test]
+    fn is_valid_git_dir_accepts_directory_with_head() {
+        let temp = tempfile::tempdir().unwrap();
+        let dot_git = temp.path().join(".git");
+        write_file(&dot_git.join("HEAD"), "ref: refs/heads/main\n");
+        assert!(is_valid_git_dir(&dot_git));
+    }
+
+    #[test]
+    fn is_valid_git_dir_accepts_git_file() {
+        let temp = tempfile::tempdir().unwrap();
+        let dot_git = temp.path().join(".git");
+        fs::write(&dot_git, "gitdir: ../real/.git/worktrees/wt\n").unwrap();
+        assert!(is_valid_git_dir(&dot_git));
+    }
+
+    #[test]
+    fn is_valid_git_dir_rejects_nonexistent() {
+        let temp = tempfile::tempdir().unwrap();
+        let dot_git = temp.path().join(".git");
+        assert!(!is_valid_git_dir(&dot_git));
+    }
+
     #[test]
     fn read_head_state_for_nested_path_uses_worktree_root() {
         let temp = tempfile::tempdir().unwrap();

src/git/repository.rs

@@ -2,7 +2,7 @@ use crate::authorship::rebase_authorship::rewrite_authorship_if_needed;
 use crate::config;
 use crate::error::GitAiError;
 use crate::git::repo_state::{
-    common_dir_for_git_dir, git_dir_for_worktree, worktree_root_for_path,
+    common_dir_for_git_dir, git_dir_for_worktree, is_valid_git_dir, worktree_root_for_path,
 };
 use crate::git::repo_storage::RepoStorage;
 use crate::git::rewrite_log::RewriteLogEvent;
@@ -2428,8 +2428,9 @@ fn has_intervening_git_dir(file_path: &Path, workdir: &Path) -> bool {
             break;
         }
         let potential_git = workdir.join(parent).join(".git");
-        if potential_git.is_dir() {
-            // A .git directory always indicates a separate independent repo.
+        if potential_git.is_dir() && is_valid_git_dir(&potential_git) {
+            // A valid .git directory (with HEAD) indicates a separate independent repo.
+            // Empty .git directories (e.g. from docker-compose volume mounts) are skipped.
             return true;
         }
         if potential_git.is_file() {
@@ -2524,7 +2525,7 @@ pub fn find_repository_for_file(
 
         // Check for .git directory or file (file for submodules/worktrees)
         let git_path = dir.join(".git");
-        if git_path.exists() {
+        if is_valid_git_dir(&git_path) {
             // Found a .git - but we need to check if this is a submodule
             // Submodules have a .git file (not directory) that points to the parent's .git/modules
             if git_path.is_file() {

tests/integration/empty_git_dir.rs

@@ -0,0 +1,85 @@
+//! Tests that an empty `.git` directory (e.g. from a docker-compose volume mount)
+//! does not fool git-ai into treating it as the repository root.
+//!
+//! Issue #1415: a user's docker-compose setup accidentally created an empty `.git`
+//! directory in a subfolder. git-ai found it first and wrote authorship notes there
+//! instead of the real repo's `.git`.
+
+use crate::repos::test_file::ExpectedLineExt;
+use crate::repos::test_repo::TestRepo;
+use std::fs;
+
+/// When a subdirectory contains an empty `.git` dir (no HEAD), checkpoints and
+/// commits should still target the real parent repository.
+#[test]
+fn empty_git_subdir_does_not_hijack_attribution() {
+    let repo = TestRepo::new();
+
+    // Bootstrap the repo with an initial commit
+    let mut readme = repo.filename("README.md");
+    readme.set_contents(crate::lines!["# Root repo"]);
+    repo.stage_all_and_commit("initial commit").unwrap();
+
+    // Create a subdirectory with an empty .git directory (simulates docker-compose
+    // accidentally creating one via a volume mount)
+    let subdir = repo.path().join("services").join("app");
+    fs::create_dir_all(subdir.join(".git")).unwrap();
+
+    // Write a file inside that subdirectory
+    let file_path = subdir.join("main.txt");
+    fs::write(&file_path, "Human line\n").unwrap();
+
+    // Fire a known-human checkpoint scoped to the file
+    repo.git_ai(&["checkpoint", "mock_known_human", "services/app/main.txt"])
+        .unwrap();
+
+    // Now simulate an AI edit
+    fs::write(&file_path, "Human line\nAI line\n").unwrap();
+    repo.git_ai(&["checkpoint", "mock_ai", "services/app/main.txt"])
+        .unwrap();
+
+    // Commit in the real repo
+    repo.stage_all_and_commit("add services/app/main.txt")
+        .unwrap();
+
+    // Verify attribution lands in the real repo, not in the empty .git
+    let mut file = repo.filename("services/app/main.txt");
+    file.assert_committed_lines(crate::lines!["Human line".human(), "AI line".ai(),]);
+}
+
+/// Verify that when the empty `.git` dir is between the file and the real repo,
+/// worktree discovery still reaches the real repo root.
+#[test]
+fn empty_git_subdir_skipped_during_worktree_discovery() {
+    let repo = TestRepo::new();
+
+    let mut readme = repo.filename("README.md");
+    readme.set_contents(crate::lines!["# Root repo"]);
+    repo.stage_all_and_commit("initial commit").unwrap();
+
+    // Empty .git in an intermediate directory
+    let intermediate = repo.path().join("packages").join("core");
+    fs::create_dir_all(intermediate.join(".git")).unwrap();
+
+    // A deeper nested file
+    let deep = intermediate.join("src");
+    fs::create_dir_all(&deep).unwrap();
+    let file_path = deep.join("lib.txt");
+
+    fs::write(&file_path, "line one\n").unwrap();
+    repo.git_ai(&[
+        "checkpoint",
+        "mock_known_human",
+        "packages/core/src/lib.txt",
+    ])
+    .unwrap();
+
+    fs::write(&file_path, "line one\nai added\n").unwrap();
+    repo.git_ai(&["checkpoint", "mock_ai", "packages/core/src/lib.txt"])
+        .unwrap();
+
+    repo.stage_all_and_commit("deep nested file").unwrap();
+
+    let mut file = repo.filename("packages/core/src/lib.txt");
+    file.assert_committed_lines(crate::lines!["line one".human(), "ai added".ai(),]);
+}

tests/integration/main.rs

@@ -52,6 +52,7 @@ mod diff_ignore_binary;
 mod droid;
 mod e2big_post_filter;
 mod e2e_user_scenarios;
+mod empty_git_dir;
 mod event_timestamp_extraction;
 mod fast_reader;
 mod fetch_notes;