Remove dangling archives in `uv cache clean ${package}` (#6915)

## Summary

Closes https://github.com/astral-sh/uv/issues/6909.

crates/uv-cache/src/lib.rs

@@ -322,10 +322,62 @@ impl Cache {
     ///
     /// Returns the number of entries removed from the cache.
     pub fn remove(&self, name: &PackageName) -> Result<Removal, io::Error> {
+        // Collect the set of referenced archives.
+        let before = {
+            let mut references = FxHashSet::default();
+            for bucket in CacheBucket::iter() {
+                let bucket = self.bucket(bucket);
+                if bucket.is_dir() {
+                    for entry in walkdir::WalkDir::new(bucket) {
+                        let entry = entry?;
+                        if entry.file_type().is_symlink() {
+                            if let Ok(target) = fs_err::canonicalize(entry.path()) {
+                                references.insert(target);
+                            }
+                        }
+                    }
+                }
+            }
+            references
+        };
+
+        // Remove any entries for the package from the cache.
         let mut summary = Removal::default();
         for bucket in CacheBucket::iter() {
             summary += bucket.remove(self, name)?;
         }
+
+        // Collect the set of referenced archives after the removal.
+        let after = {
+            let mut references = FxHashSet::default();
+            for bucket in CacheBucket::iter() {
+                let bucket = self.bucket(bucket);
+                if bucket.is_dir() {
+                    for entry in walkdir::WalkDir::new(bucket) {
+                        let entry = entry?;
+                        if entry.file_type().is_symlink() {
+                            if let Ok(target) = fs_err::canonicalize(entry.path()) {
+                                references.insert(target);
+                            }
+                        }
+                    }
+                }
+            }
+            references
+        };
+
+        if before != after {
+            // Remove any archives that are no longer referenced.
+            for entry in fs::read_dir(self.bucket(CacheBucket::Archive))? {
+                let entry = entry?;
+                let path = fs_err::canonicalize(entry.path())?;
+                if !after.contains(&path) && before.contains(&path) {
+                    debug!("Removing dangling cache entry: {}", path.display());
+                    summary += rm_rf(path)?;
+                }
+            }
+        }
+
         Ok(summary)
     }
 

crates/uv/tests/cache_clean.rs

@@ -65,14 +65,27 @@ fn clean_package_pypi() -> Result<()> {
         "Expected the `.rkyv` file to exist for `iniconfig`"
     );
 
-    uv_snapshot!(context.filters(), context.clean().arg("--verbose").arg("iniconfig"), @r###"
+    let filters: Vec<_> = context
+        .filters()
+        .into_iter()
+        .chain([
+            // The cache entry does not have a stable key, so we filter it out
+            (
+                r"\[CACHE_DIR\](\\|\/)(.+)(\\|\/).*",
+                "[CACHE_DIR]/$2/[ENTRY]",
+            ),
+        ])
+        .collect();
+
+    uv_snapshot!(&filters, context.clean().arg("--verbose").arg("iniconfig"), @r###"
     success: true
     exit_code: 0
     ----- stdout -----
 
     ----- stderr -----
     DEBUG uv [VERSION] ([COMMIT] DATE)
-    Removed 4 files for iniconfig ([SIZE])
+    DEBUG Removing dangling cache entry: [CACHE_DIR]/archive-v0/[ENTRY]
+    Removed 13 files for iniconfig ([SIZE])
     "###);
 
     // Assert that the `.rkyv` file is removed for `iniconfig`.
@@ -81,6 +94,18 @@ fn clean_package_pypi() -> Result<()> {
         "Expected the `.rkyv` file to be removed for `iniconfig`"
     );
 
+    // Running `uv cache prune` should have no effect.
+    uv_snapshot!(&filters, context.prune().arg("--verbose"), @r###"
+    success: true
+    exit_code: 0
+    ----- stdout -----
+
+    ----- stderr -----
+    DEBUG uv [VERSION] ([COMMIT] DATE)
+    Pruning cache at: [CACHE_DIR]/
+    No unused entries found
+    "###);
+
     Ok(())
 }
 
@@ -113,14 +138,27 @@ fn clean_package_index() -> Result<()> {
         "Expected the `.rkyv` file to exist for `iniconfig`"
     );
 
-    uv_snapshot!(context.filters(), context.clean().arg("--verbose").arg("iniconfig"), @r###"
+    let filters: Vec<_> = context
+        .filters()
+        .into_iter()
+        .chain([
+            // The cache entry does not have a stable key, so we filter it out
+            (
+                r"\[CACHE_DIR\](\\|\/)(.+)(\\|\/).*",
+                "[CACHE_DIR]/$2/[ENTRY]",
+            ),
+        ])
+        .collect();
+
+    uv_snapshot!(&filters, context.clean().arg("--verbose").arg("iniconfig"), @r###"
     success: true
     exit_code: 0
     ----- stdout -----
 
     ----- stderr -----
     DEBUG uv [VERSION] ([COMMIT] DATE)
-    Removed 4 files for iniconfig ([SIZE])
+    DEBUG Removing dangling cache entry: [CACHE_DIR]/archive-v0/[ENTRY]
+    Removed 13 files for iniconfig ([SIZE])
     "###);
 
     // Assert that the `.rkyv` file is removed for `iniconfig`.

crates/uv/tests/pip_sync.rs

@@ -1396,7 +1396,7 @@ fn install_url_source_dist_cached() -> Result<()> {
     ----- stdout -----
 
     ----- stderr -----
-    Removed 13 files for source-distribution ([SIZE])
+    Removed 19 files for source-distribution ([SIZE])
     "###
     );
 
@@ -1591,7 +1591,7 @@ fn install_registry_source_dist_cached() -> Result<()> {
     ----- stdout -----
 
     ----- stderr -----
-    Removed 14 files for source-distribution ([SIZE])
+    Removed 20 files for source-distribution ([SIZE])
     "###
     );
 
@@ -1687,7 +1687,7 @@ fn install_path_source_dist_cached() -> Result<()> {
     ----- stdout -----
 
     ----- stderr -----
-    Removed 13 files for source-distribution ([SIZE])
+    Removed 19 files for source-distribution ([SIZE])
     "###
     );
 
@@ -1788,7 +1788,7 @@ fn install_path_built_dist_cached() -> Result<()> {
     ----- stdout -----
 
     ----- stderr -----
-    Removed 2 files for tomli ([SIZE])
+    Removed 11 files for tomli ([SIZE])
     "###
     );
 
@@ -1876,7 +1876,7 @@ fn install_url_built_dist_cached() -> Result<()> {
     ----- stdout -----
 
     ----- stderr -----
-    Removed 3 files for tqdm ([SIZE])
+    Removed 43 files for tqdm ([SIZE])
     "###
     );