From 1ea9fdb21af20836b3915a429222b7187325a787 Mon Sep 17 00:00:00 2001
From: Matt Van Horn <455140+mvanhorn@users.noreply.github.com>
Date: Thu, 3 Sep 2026 04:32:31 -0700
Subject: [PATCH] fix: stage deleted files with libgit2

Fixes #638
---
 src/vcs/git/staging.rs | 54 +++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 53 insertions(+), 1 deletion(-)

diff --git a/src/vcs/git/staging.rs b/src/vcs/git/staging.rs
index f73e0a49..ab397d8a 100644
--- a/src/vcs/git/staging.rs
+++ b/src/vcs/git/staging.rs
@@ -5,7 +5,14 @@ use crate::error::Result;
 
 pub fn stage_file(repo: &Repository, path: &Path) -> Result<()> {
     let mut index = repo.index()?;
-    index.add_path(path)?;
+    if repo
+        .workdir()
+        .is_some_and(|workdir| workdir.join(path).exists())
+    {
+        index.add_path(path)?;
+    } else {
+        index.remove_path(path)?;
+    }
     index.write()?;
     Ok(())
 }
@@ -15,6 +22,25 @@ mod tests {
     use super::*;
     use std::fs;
 
+    fn create_initial_commit(repo: &Repository, file_name: &str, content: &str) {
+        fs::write(repo.workdir().unwrap().join(file_name), content)
+            .expect("failed to write initial file");
+
+        let mut index = repo.index().expect("failed to open index");
+        index
+            .add_path(Path::new(file_name))
+            .expect("failed to add file to index");
+        index.write().expect("failed to write index");
+
+        let tree_id = index.write_tree().expect("failed to write tree");
+        let tree = repo.find_tree(tree_id).expect("failed to find tree");
+        let sig = git2::Signature::now("Test User", "test@example.com")
+            .expect("failed to create signature");
+
+        repo.commit(Some("HEAD"), &sig, &sig, "initial", &tree, &[])
+            .expect("failed to create commit");
+    }
+
     #[test]
     fn stage_file_adds_to_index() {
         let temp_dir = tempfile::tempdir().expect("failed to create temp dir");
@@ -28,4 +54,30 @@ mod tests {
         let index = repo.index().unwrap();
         assert!(index.get_path(Path::new("test.txt"), 0).is_some());
     }
+
+    #[test]
+    fn stage_file_removes_deleted_file_from_index() {
+        let temp_dir = tempfile::tempdir().expect("failed to create temp dir");
+        let repo = Repository::init(temp_dir.path()).expect("failed to init repo");
+        create_initial_commit(&repo, "deleted.txt", "goodbye\n");
+
+        fs::remove_file(temp_dir.path().join("deleted.txt")).expect("failed to delete file");
+
+        stage_file(&repo, Path::new("deleted.txt")).unwrap();
+
+        let reopened_repo = Repository::open(temp_dir.path()).expect("failed to reopen repo");
+        let index = reopened_repo.index().expect("failed to reopen index");
+        assert!(index.get_path(Path::new("deleted.txt"), 0).is_none());
+
+        let head_tree = reopened_repo
+            .head()
+            .expect("failed to find HEAD")
+            .peel_to_tree()
+            .expect("failed to find HEAD tree");
+        let diff = reopened_repo
+            .diff_tree_to_index(Some(&head_tree), Some(&index), None)
+            .expect("failed to diff HEAD against index");
+        let delta = diff.deltas().next().expect("expected staged deletion");
+        assert_eq!(delta.status(), git2::Delta::Deleted);
+    }
 }