diff --git a/src/main.rs b/src/main.rs
index 6c23393..abf79eb 100755
--- a/src/main.rs
+++ b/src/main.rs
@@ -160,12 +160,32 @@ fn main() {
 
     if let true = matches.is_present("reinit") {
         let config = workspace::read_cfg();
-        Command::new("bash")
-            .args(&["-c", "rm -rf */"])
+        let out = Command::new("bash")
+            .args(&["-c", "ls -A"])
+            .output()
+            .unwrap()
+            .stdout;
+        let dirs_to_s = String::from_utf8_lossy(&*out);
+        let mut dirs = dirs_to_s.lines().collect::<Vec<&str>>();
+
+        let name = config.name.unwrap();
+
+        dirs.retain(|x| *x != "mlc.toml");
+        dirs.retain(|x| *x != ".git");
+        if config.mode == "repository" {
+            dirs.retain(|x| *x != "out");
+            dirs.retain(|x| *x != name);
+        }
+
+        info("Removing all repo directories to reinitialise".to_string());
+
+        Command::new("rm")
+            .args(&["-rf", &dirs.join(" ")])
             .spawn()
             .unwrap()
             .wait()
             .unwrap();
+
         if config.mode == "workspace" {
             for r in config.repo {
                 info(format!("Cloning (workspace mode): {}", r));