diff --git a/hive-c0re/src/forge/repos.rs b/hive-c0re/src/forge/repos.rs
index b2500b48..0985410e 100644
--- a/hive-c0re/src/forge/repos.rs
+++ b/hive-c0re/src/forge/repos.rs
@@ -2,6 +2,8 @@
 //! `agent-configs/<name>`. The typed API-client constructor + org-name
 //! constants live in the module root (`super`).
 
+use std::path::Path;
+
 use super::{CONFIG_ORG, forge_git_url, reader_token};
 
 /// Seed an agent's `applied` repo, missing its `.git` entirely (first spawn,
@@ -15,7 +17,7 @@ use super::{CONFIG_ORG, forge_git_url, reader_token};
 /// forge has no `main` for the agent yet (the normal case right after
 /// `swarm-controller` creates it, before it has pushed anything), or any git
 /// step fails. Callers fall back to the template or the original hard error. A
-/// failed seed leaves no `.git` behind, so a later "is it seeded" check reads
+/// failed seed leaves the directory empty, so a later "is it seeded" check reads
 /// the same as before the attempt. Only `true` once `applied` is seeded and
 /// tagged `deployed/0`.
 pub async fn fetch_config_main_into_applied(name: &str) -> bool {
@@ -79,7 +81,42 @@ pub async fn fetch_config_main_into_applied(name: &str) -> bool {
     }
     .await;
     if !seeded {
-        let _ = std::fs::remove_dir_all(applied.join(".git"));
+        clear_dir(&applied);
     }
     seeded
 }
+
+/// Empty `dir`, keeping the directory itself: a failed seed may have written
+/// the working tree as well as the `.git`, and the template fallback must start
+/// from nothing rather than adopt files that were meant for the forge's commit.
+fn clear_dir(dir: &Path) {
+    let Ok(entries) = std::fs::read_dir(dir) else {
+        return;
+    };
+    for entry in entries.flatten() {
+        let path = entry.path();
+        let _ = if path.is_dir() {
+            std::fs::remove_dir_all(path)
+        } else {
+            std::fs::remove_file(path)
+        };
+    }
+}
+
+#[cfg(test)]
+mod tests {
+    use super::clear_dir;
+
+    #[test]
+    fn clear_dir_empties_a_dir_but_keeps_it() {
+        let dir = tempfile::tempdir().expect("tempdir");
+        std::fs::create_dir(dir.path().join(".git")).expect("mkdir .git");
+        std::fs::write(dir.path().join(".git/HEAD"), "ref").expect("write HEAD");
+        std::fs::write(dir.path().join("agent.nix"), "{}").expect("write agent.nix");
+
+        clear_dir(dir.path());
+
+        assert!(dir.path().is_dir(), "the directory itself stays");
+        assert_eq!(std::fs::read_dir(dir.path()).expect("read_dir").count(), 0);
+    }
+}