diff --git a/src/commands/add.rs b/src/commands/add.rs
index 5af62ae..32e0b14 100644
--- a/src/commands/add.rs
+++ b/src/commands/add.rs
@@ -49,20 +49,20 @@ fn collect_files_recursively(dir: &PathBuf) -> Result<Vec<PathBuf>> {
 /// Main function for the `guts add` command
 /// Adds files to the staging area (index)
 pub fn run(args: &AddArgs) -> Result<String> {
+    // Determine current directory to use
+    let current_dir = args
+        .dir
+        .clone()
+        .unwrap_or_else(|| std::env::current_dir().expect("failed to get current directory"));
+
     // Check if we're in a git repository
-    if !simple_index::is_git_repository()? {
+    if !simple_index::is_git_repository_from(Some(&current_dir))? {
         return Err(anyhow!("fatal: not a git repository"));
     }
 
     let mut added_files = Vec::new();
     let mut output = String::new();
 
-    // Determine current directory to use
-    let current_dir = args
-        .dir
-        .clone()
-        .unwrap_or_else(|| std::env::current_dir().expect("failed to get current directory"));
-
     // Load .gutsignore matcher
     let matcher = IgnoreMatcher::from_gutsignore(&current_dir)
         .unwrap_or_else(|_| IgnoreMatcher::empty());
@@ -76,7 +76,7 @@ pub fn run(args: &AddArgs) -> Result<String> {
                 if matcher.is_ignored(&file, &current_dir) {
                     continue;
                 }
-                simple_index::add_file_to_index(&file)?;
+                simple_index::add_file_to_index_from(&file, Some(&current_dir))?;
                 added_files.push(file.display().to_string());
             }
             continue;
@@ -97,7 +97,7 @@ pub fn run(args: &AddArgs) -> Result<String> {
                 if matcher.is_ignored(&file, &current_dir) {
                     continue;
                 }
-                simple_index::add_file_to_index(&file)?;
+                simple_index::add_file_to_index_from(&file, Some(&current_dir))?;
                 added_files.push(file.display().to_string());
             }
         } else {
@@ -106,7 +106,7 @@ pub fn run(args: &AddArgs) -> Result<String> {
                 continue;
             }
             // Add the file to the JSON index
-            simple_index::add_file_to_index(file_path)?;
+            simple_index::add_file_to_index_from(file_path, Some(&current_dir))?;
             added_files.push(file_path.display().to_string());
         }
     }
diff --git a/src/commands/commit.rs b/src/commands/commit.rs
index 0476fd9..3769aeb 100644
--- a/src/commands/commit.rs
+++ b/src/commands/commit.rs
@@ -35,7 +35,7 @@ pub fn run(args: &CommitArgs) -> Result<String> {
 
 fn run_commit(args: &CommitArgs) -> Result<String> {
     // Check if we're in a git repository
-    if !simple_index::is_git_repository()? {
+    if !simple_index::is_git_repository_from(args.dir.as_ref())? {
         return Err(anyhow::anyhow!("fatal: not a git repository"));
     }
 
diff --git a/src/commands/log.rs b/src/commands/log.rs
index ecf7e57..2ae4f5f 100644
--- a/src/commands/log.rs
+++ b/src/commands/log.rs
@@ -22,7 +22,7 @@ pub fn run(args: &LogArgs) -> Result<String> {
         .unwrap_or_else(|| std::env::current_dir().expect("failed to get current directory"));
 
     // Check if we're in a git repository
-    if !simple_index::is_git_repository()? {
+    if !simple_index::is_git_repository_from(args.dir.as_ref())? {
         return Err(anyhow!("fatal: not a git repository"));
     }
 
diff --git a/src/commands/rm.rs b/src/commands/rm.rs
index 6af113e..b474003 100644
--- a/src/commands/rm.rs
+++ b/src/commands/rm.rs
@@ -49,7 +49,7 @@ fn remove_file_from_index(file_path: &PathBuf) -> Result<bool> {
 /// Removes files from working directory and index
 pub fn run(args: &RmArgs) -> Result<String> {
     // Check if we're in a git repository
-    if !simple_index::is_git_repository()? {
+    if !simple_index::is_git_repository_from(args.dir.as_ref())? {
         return Err(anyhow!("fatal: not a git repository"));
     }
 
diff --git a/src/commands/status.rs b/src/commands/status.rs
index de5f46e..3f62035 100644
--- a/src/commands/status.rs
+++ b/src/commands/status.rs
@@ -19,15 +19,15 @@ pub fn run(args: &StatusObject) -> Result<String> {
         .clone()
         .unwrap_or_else(|| std::env::current_dir().expect("failed to get current directory"));
 
-    if !simple_index::is_git_repository()? {
+    if !simple_index::is_git_repository_from(Some(&current_dir))? {
         return Ok("fatal: not a git repository".to_string());
     }
 
     let matcher = IgnoreMatcher::from_gutsignore(&current_dir)
         .unwrap_or_else(|_| IgnoreMatcher::empty());
 
-    let committed_files = simple_index::get_committed_files()?;
-    let index = simple_index::SimpleIndex::load()?;
+    let committed_files = simple_index::get_committed_files_from(Some(&current_dir))?;
+    let index = simple_index::SimpleIndex::load_from(Some(&current_dir))?;
     let work_files = list_working_dir_files(&current_dir, &matcher)?;
 
     let current_branch = read_head::get_current_branch()
@@ -154,9 +154,11 @@ fn list_working_dir_files(current_dir: &PathBuf, matcher: &IgnoreMatcher) -> Res
 }
 
 fn get_relative_path(file_path: &PathBuf, current_dir: &PathBuf) -> Result<String> {
+    // Find repo root from current directory context
+    let repo_root = simple_index::find_repo_root_from(Some(current_dir))?;
     let relative = file_path
-        .strip_prefix(current_dir)
-        .map_err(|_| anyhow::anyhow!("file is not in the current directory"))?;
+        .strip_prefix(&repo_root)
+        .map_err(|_| anyhow::anyhow!("file is not in the repository"))?;
     Ok(relative.to_string_lossy().to_string())
 }
 
diff --git a/src/commands/write_tree.rs b/src/commands/write_tree.rs
index 7aa12c0..0d00542 100644
--- a/src/commands/write_tree.rs
+++ b/src/commands/write_tree.rs
@@ -11,9 +11,9 @@ pub struct WriteTreeArgs {
 
 /// New version of write-tree that uses the simple JSON index
 /// Instead of reading the filesystem, reads the index to create the tree
-pub fn run(_args: &WriteTreeArgs) -> Result<String> {
+pub fn run(args: &WriteTreeArgs) -> Result<String> {
     // Check if we're in a git repository
-    if !simple_index::is_git_repository()? {
+    if !simple_index::is_git_repository_from(args.dir.as_ref())? {
         return Err(anyhow::anyhow!("fatal: not a git repository"));
     }
 
diff --git a/src/core/simple_index.rs b/src/core/simple_index.rs
index 350d54e..2b2c1d6 100644
--- a/src/core/simple_index.rs
+++ b/src/core/simple_index.rs
@@ -35,6 +35,23 @@ impl SimpleIndex {
         Ok(index)
     }
 
+    /// Load index from .git/simple_index.json from a specific directory
+    pub fn load_from(start_dir: Option<&PathBuf>) -> Result<Self> {
+        let index_path = get_simple_index_path_from(start_dir)?;
+
+        if !index_path.exists() {
+            return Ok(SimpleIndex::default());
+        }
+
+        let content = fs::read_to_string(&index_path)
+            .with_context(|| format!("unable to read {:?}", index_path))?;
+
+        let index: SimpleIndex =
+            serde_json::from_str(&content).with_context(|| "invalid JSON in index")?;
+
+        Ok(index)
+    }
+
     /// Save index to .git/simple_index.json
     pub fn save(&self) -> Result<()> {
         let index_path = get_simple_index_path()?;
@@ -108,6 +125,12 @@ fn get_simple_index_path() -> Result<PathBuf> {
     Ok(repo_root.join(".git").join("simple_index.json"))
 }
 
+/// Return path to .git/simple_index.json from a specific directory
+fn get_simple_index_path_from(start_dir: Option<&PathBuf>) -> Result<PathBuf> {
+    let repo_root = find_repo_root_from(start_dir)?;
+    Ok(repo_root.join(".git").join("simple_index.json"))
+}
+
 /// Convert absolute path to relative path from repo root
 fn get_relative_path(file_path: &Path) -> Result<String> {
     let repo_root = find_repo_root()?;
@@ -245,3 +268,101 @@ fn decompress_object(data: &[u8]) -> Result<Vec<u8>> {
         }
     }
 }
+
+/// Find Git repository root from a specific directory
+pub fn find_repo_root_from(start_dir: Option<&PathBuf>) -> Result<PathBuf> {
+    let mut current = match start_dir {
+        Some(dir) => dir.clone(),
+        None => std::env::current_dir().with_context(|| "unable to get current directory")?,
+    };
+
+    loop {
+        let git_dir = current.join(".git");
+        if git_dir.exists() && git_dir.is_dir() {
+            return Ok(current);
+        }
+
+        match current.parent() {
+            Some(parent) => current = parent.to_path_buf(),
+            None => return Err(anyhow!("not a git repository")),
+        }
+    }
+}
+
+/// Check if we're in a Git repository from a specific directory
+pub fn is_git_repository_from(start_dir: Option<&PathBuf>) -> Result<bool> {
+    match find_repo_root_from(start_dir) {
+        Ok(_) => Ok(true),
+        Err(_) => Ok(false),
+    }
+}
+
+/// Add a file to the index from a specific directory context
+pub fn add_file_to_index_from(file_path: &Path, start_dir: Option<&PathBuf>) -> Result<()> {
+    // Set current directory context if provided
+    let original_dir = std::env::current_dir()?;
+    
+    if let Some(dir) = start_dir {
+        std::env::set_current_dir(dir)?;
+    }
+    
+    // Use existing add_file_to_index function
+    let result = add_file_to_index(file_path);
+    
+    // Restore original directory
+    std::env::set_current_dir(&original_dir)?;
+    
+    result
+}
+
+/// Get the files committed in the current HEAD from a specific directory
+/// Returns a HashMap: relative file path -> SHA-1 hash
+pub fn get_committed_files_from(start_dir: Option<&PathBuf>) -> Result<HashMap<String, String>> {
+    let repo_root = find_repo_root_from(start_dir)?;
+    let git_dir = repo_root.join(".git");
+    
+    // Read HEAD to get current commit
+    let head_path = git_dir.join("HEAD");
+    if !head_path.exists() {
+        // No commits yet
+        return Ok(HashMap::new());
+    }
+    
+    let head_content = fs::read_to_string(&head_path)?;
+    let head_content = head_content.trim();
+    
+    // Get the commit hash
+    let commit_hash = if head_content.starts_with("ref: ") {
+        // HEAD points to a branch
+        let ref_path = head_content.strip_prefix("ref: ").unwrap();
+        let ref_file = git_dir.join(ref_path);
+        
+        if !ref_file.exists() {
+            // Branch exists but no commits yet
+            return Ok(HashMap::new());
+        }
+        
+        fs::read_to_string(ref_file)?.trim().to_string()
+    } else {
+        // Detached HEAD, direct commit hash
+        head_content.to_string()
+    };
+    
+    // Read the commit object to get the tree hash
+    let commit_obj_path = cat::get_object_path(&git_dir, &commit_hash);
+    if !commit_obj_path.exists() {
+        return Ok(HashMap::new());
+    }
+    
+    let commit_data = fs::read(&commit_obj_path)?;
+    let decompressed = decompress_object(&commit_data)?;
+    let parsed = cat::parse_object(&decompressed)?;
+    
+    let tree_hash = match parsed {
+        cat::ParsedObject::Commit(commit) => commit.tree,
+        _ => return Err(anyhow!("HEAD does not point to a commit object")),
+    };
+    
+    // Read the tree object to get the files
+    get_files_from_tree(&git_dir, &tree_hash, "")
+}
diff --git a/src/terminal/app.rs b/src/terminal/app.rs
index 307e22c..83f75b5 100644
--- a/src/terminal/app.rs
+++ b/src/terminal/app.rs
@@ -329,7 +329,7 @@ impl App {
         }
 
         // Sinon, commande système via shell
-        let _cleaned_dir = if self.current_dir.starts_with(r"\\?\") {
+        let cleaned_dir = if self.current_dir.starts_with(r"\\?\") {
             self.current_dir.trim_start_matches(r"\\?\\").to_string()
         } else {
             self.current_dir.clone()
@@ -346,7 +346,7 @@ impl App {
         let shell_result = std::process::Command::new("sh")
             .arg("-c")
             .arg(&command)
-            .current_dir(&self.current_dir)
+            .current_dir(&cleaned_dir)
             .output();
 
         let result = match shell_result {