Fix Windows: use dunce::canonicalize to avoid \\?\ UNC paths

Root cause: std::fs::canonicalize on Windows produces \\?\ prefixed
paths that libgit2 mishandles during repository discovery and diffing,
and that cause path mismatches in cargo metadata output.

Fixes:
- Use dunce::canonicalize instead of std::fs::canonicalize in CLI
  (dunce strips the \\?\ prefix when safe to do so)
- Refresh git index from disk before computing diffs to pick up
  changes made by external git CLI commands

Author: Rani367

Cargo.toml

@@ -25,6 +25,7 @@ clap_complete = "4"
 git2 = "0.20"
 petgraph = "0.7"
 colored = "3"
+dunce = "1"
 which = "7"
 glob = "0.3"
 tracing = "0.1"

crates/affected-cli/Cargo.toml

@@ -24,6 +24,7 @@ anyhow.workspace = true
 serde_json.workspace = true
 serde.workspace = true
 colored.workspace = true
+dunce.workspace = true
 tracing.workspace = true
 tracing-subscriber.workspace = true
 indicatif.workspace = true

crates/affected-cli/src/main.rs

@@ -208,7 +208,7 @@ fn main() -> Result<()> {
         .without_time()
         .init();
 
-    let root = std::fs::canonicalize(&cli.root)?;
+    let root = dunce::canonicalize(&cli.root)?;
 
     match cli.command {
         Commands::Test {

crates/affected-core/Cargo.toml

@@ -17,6 +17,7 @@ anyhow.workspace = true
 serde.workspace = true
 serde_json.workspace = true
 toml.workspace = true
+dunce.workspace = true
 git2.workspace = true
 petgraph.workspace = true
 which.workspace = true

crates/affected-core/src/git.rs

@@ -9,23 +9,9 @@ pub struct GitDiff {
     pub repo_root: PathBuf,
 }
 
-/// Strip the `\\?\` extended-length path prefix on Windows.
-/// libgit2 mishandles these paths, causing discovery and diff failures.
-fn normalize_path(path: &Path) -> PathBuf {
-    #[cfg(windows)]
-    {
-        let s = path.to_string_lossy();
-        if let Some(stripped) = s.strip_prefix(r"\\?\") {
-            return PathBuf::from(stripped);
-        }
-    }
-    path.to_path_buf()
-}
-
 /// Compute changed files between a base ref and HEAD (plus uncommitted changes).
 pub fn changed_files(repo_path: &Path, base_ref: &str) -> Result<GitDiff> {
-    let normalized = normalize_path(repo_path);
-    let repo = Repository::discover(&normalized).context("Not a git repository")?;
+    let repo = Repository::discover(repo_path).context("Not a git repository")?;
 
     let repo_root = repo
         .workdir()
@@ -51,7 +37,9 @@ pub fn changed_files(repo_path: &Path, base_ref: &str) -> Result<GitDiff> {
 
     // Refresh index from disk to pick up changes made by the git CLI
     let mut index = repo.index().context("Could not read index")?;
-    index.read(true).context("Could not refresh index from disk")?;
+    index
+        .read(true)
+        .context("Could not refresh index from disk")?;
 
     let mut files = HashSet::new();
 
@@ -97,8 +85,7 @@ pub fn changed_files(repo_path: &Path, base_ref: &str) -> Result<GitDiff> {
 /// Compute the merge-base between HEAD and the given branch.
 /// Returns the commit SHA as a string. Used when `--merge-base` is passed.
 pub fn merge_base(repo_path: &Path, branch: &str) -> Result<String> {
-    let normalized = normalize_path(repo_path);
-    let repo = Repository::discover(&normalized).context("Not a git repository")?;
+    let repo = Repository::discover(repo_path).context("Not a git repository")?;
 
     debug!("Computing merge-base between HEAD and '{}'", branch);