diff --git a/crates/dashboard-core/src/config.rs b/crates/dashboard-core/src/config.rs
index 42739dd..a377a3d 100644
--- a/crates/dashboard-core/src/config.rs
+++ b/crates/dashboard-core/src/config.rs
@@ -222,8 +222,8 @@ impl Config {
     }
 }
 
-/// The git checkouts directly under `root`, sorted by path. Only primary checkouts (a `.git` folder) count: a linked
-/// worktree (a `.git` file) is already part of its primary checkout's status.
+/// The git checkouts directly under `root`, sorted by path. Only primary checkouts count: a `.git` folder, or a `.git`
+/// file pointing at a git folder of its own. A linked worktree is already part of its primary checkout's status.
 pub fn discover(root: &Path) -> Vec<PathBuf> {
     let Ok(entries) = std::fs::read_dir(root) else {
         return Vec::new();
@@ -231,12 +231,41 @@ pub fn discover(root: &Path) -> Vec<PathBuf> {
     let mut found: Vec<PathBuf> = entries
         .filter_map(Result::ok)
         .map(|entry| entry.path())
-        .filter(|path| path.is_dir() && path.join(".git").is_dir())
+        .filter(|path| path.is_dir() && is_primary_checkout(path))
         .collect();
     found.sort();
     found
 }
 
+/// The most a `.git` file is read: its one `gitdir:` line, with room for a long path.
+const MAX_GIT_FILE: u64 = 64 * 1024;
+
+/// Whether `checkout`'s `.git` is a folder, or a `gitdir: <path>` file whose git folder is its own, as
+/// `git clone --separate-git-dir` makes (#88). A linked worktree's git folder holds `commondir`, pointing at the
+/// primary's. Anything else, such as an unreadable, oversized or malformed `.git` file, a target that isn't a git
+/// folder, or a `.git` that is neither a folder nor a regular file, is skipped. Nothing here starts git.
+fn is_primary_checkout(checkout: &Path) -> bool {
+    use std::io::Read as _;
+    let marker = checkout.join(".git");
+    let Ok(metadata) = std::fs::metadata(&marker) else {
+        return false;
+    };
+    if metadata.is_dir() {
+        return true;
+    }
+    // A pipe or device could block a read, and a huge file isn't a `.git` file.
+    if !metadata.is_file() || metadata.len() > MAX_GIT_FILE {
+        return false;
+    }
+    let mut pointer = String::new();
+    let read = std::fs::File::open(&marker).and_then(|file| file.take(MAX_GIT_FILE).read_to_string(&mut pointer));
+    let Some(target) = read.ok().and_then(|_| pointer.trim().strip_prefix("gitdir: ")) else {
+        return false;
+    };
+    let git_dir = checkout.join(target.trim());
+    git_dir.join("HEAD").is_file() && !git_dir.join("commondir").exists()
+}
+
 /// Notices edits to `config.toml` while the app runs (#21) by comparing its bytes with the last applied read. The
 /// file is a few hundred bytes, so reading it every couple of seconds is cheap, and unlike a timestamp and size it
 /// can't miss a same-length edit. An unchanged file is never parsed again.
diff --git a/crates/dashboard-core/tests/storage.rs b/crates/dashboard-core/tests/storage.rs
index f2c6d73..fb7f39c 100644
--- a/crates/dashboard-core/tests/storage.rs
+++ b/crates/dashboard-core/tests/storage.rs
@@ -104,6 +104,88 @@ fn first_run_discovers_checkouts_one_level_under_the_root_and_writes_them() {
     assert!(dir.join(config::FILE_NAME).is_file());
 }
 
+/// A git folder for a `.git` file to point at: `HEAD`, plus `commondir` when it belongs to a linked worktree.
+fn git_dir(path: &Path, linked: bool) {
+    std::fs::create_dir_all(path).unwrap();
+    std::fs::write(path.join("HEAD"), "ref: refs/heads/main\n").unwrap();
+    if linked {
+        std::fs::write(path.join("commondir"), "../..\n").unwrap();
+    }
+}
+
+fn git_file(root: &Path, name: &str, contents: &[u8]) {
+    std::fs::create_dir_all(root.join(name)).unwrap();
+    std::fs::write(root.join(name).join(".git"), contents).unwrap();
+}
+
+#[test]
+fn first_run_discovers_separate_git_dir_checkouts_but_not_worktrees_or_broken_git_files() {
+    let scratch = Scratch::new("first-run-separate");
+    let root = scratch.path().join("github");
+    let gitdirs = scratch.path().join("gitdirs");
+    std::fs::create_dir_all(root.join("plain/.git")).unwrap();
+    // `git clone --separate-git-dir`: the .git file points at a git folder of its own, absolute or relative.
+    git_dir(&gitdirs.join("sep.git"), false);
+    git_file(
+        &root,
+        "separate",
+        format!("gitdir: {}\n", gitdirs.join("sep.git").display()).as_bytes(),
+    );
+    git_dir(&gitdirs.join("rel.git"), false);
+    git_file(&root, "relative", b"gitdir: ../../gitdirs/rel.git\r\n");
+    // Not checkouts. A linked worktree's git folder has HEAD too; commondir is what tells it apart.
+    let worktree = root.join("plain/.git/worktrees/pr-1");
+    git_dir(&worktree, true);
+    git_file(
+        &root,
+        "plain-pr-1",
+        format!("gitdir: {}", worktree.display()).as_bytes(),
+    );
+    git_file(
+        &root,
+        "missing",
+        format!("gitdir: {}", gitdirs.join("none.git").display()).as_bytes(),
+    );
+    std::fs::create_dir_all(gitdirs.join("no-head.git")).unwrap();
+    git_file(
+        &root,
+        "no-head",
+        format!("gitdir: {}", gitdirs.join("no-head.git").display()).as_bytes(),
+    );
+    git_file(
+        &root,
+        "malformed",
+        format!("{}\n", gitdirs.join("sep.git").display()).as_bytes(),
+    );
+    git_file(&root, "empty", b"");
+    git_file(&root, "not-utf8", b"gitdir: \xff\xfe\n");
+    // A valid first line, but more than a .git file holds: never read.
+    let mut huge = format!("gitdir: {}\n", gitdirs.join("sep.git").display()).into_bytes();
+    huge.resize(70 * 1024, b' ');
+    git_file(&root, "huge", &huge);
+    std::fs::create_dir_all(root.join("group/deep/.git")).unwrap();
+    #[cfg(target_os = "linux")]
+    {
+        // A pipe is never opened: reading one with no writer would block discovery.
+        std::fs::create_dir_all(root.join("pipe")).unwrap();
+        let fifo = rustix::fs::FileType::Fifo;
+        rustix::fs::mknodat(rustix::fs::CWD, root.join("pipe/.git"), fifo, 0o600.into(), 0).unwrap();
+    }
+
+    let expected = [root.join("plain"), root.join("relative"), root.join("separate")];
+    assert_eq!(config::discover(&root), expected);
+    let config = Config::load_or_create_in(&scratch.path().join("config"), root.clone()).unwrap();
+    assert_eq!(config.repositories, expected);
+}
+
+#[test]
+fn discovery_of_a_missing_root_or_a_file_is_empty() {
+    let scratch = Scratch::new("first-run-no-root");
+    assert!(config::discover(&scratch.path().join("absent")).is_empty());
+    std::fs::write(scratch.path().join("file"), "").unwrap();
+    assert!(config::discover(&scratch.path().join("file")).is_empty());
+}
+
 #[test]
 fn cache_round_trips_and_drops_removed_repositories() {
     let scratch = Scratch::new("cache");