fix(patch): reuse the existing patch of a git-hosted dependency (#15666)

`pnpm patch-commit` records the patch of a git-hosted package under
`name@version`, but `pnpm patch` looked the existing patch up under
`name@<tarball URL>`, the bare specifier it picks for such a package.
The lookup never matched, so re-running `pnpm patch` gave a clean copy
without the committed changes.

Fall back to `name@version` when the bare specifier finds no patch, in
both the TypeScript and the Rust CLI.

Closes https://github.com/pnpm/pnpm/issues/9699

Co-authored-by: Claude Opus 5.5 (1M context) <noreply@anthropic.com>

.changeset/repatch-git-hosted-dependency.md

@@ -0,0 +1,7 @@
+---
+"@pnpm/patching.commands": patch
+"pnpm": patch
+"pacquet": patch
+---
+
+`pnpm patch` now applies the existing patch file to the edit directory of a git-hosted dependency, as it already does for packages from the registry [#9699](https://github.com/pnpm/pnpm/issues/9699).

pnpm/crates/cli/src/cli_args/patch/paths.rs

@@ -1,6 +1,7 @@
 use super::{
     Component, PatchError, PatchTarget, Path, PathBuf, fs, io, is_subdir, lexical_normalize,
 };
+use indexmap::IndexMap;
 
 pub(super) fn resolve_path(dir: &Path, path: &Path) -> PathBuf {
     if path.is_absolute() { path.to_path_buf() } else { dir.join(path) }
@@ -163,15 +164,9 @@ pub(super) fn apply_existing_patch_file(
     edit_dir: &Path,
 ) -> Result<(), PatchError> {
     let Some(patched_dependencies) = &config.patched_dependencies else { return Ok(()) };
-    let exact_key = format!("{}@{}", target.alias, target.bare_specifier);
-    let patch_file = patched_dependencies
-        .get(&exact_key)
-        .or_else(|| {
-            target.apply_to_all
-                .then(|| patched_dependencies.get(&target.alias))
-                .flatten()
-        });
-    let Some(patch_file) = patch_file else { return Ok(()) };
+    let Some(patch_file) = find_existing_patch_file(patched_dependencies, target) else {
+        return Ok(());
+    };
     let base_dir = config.workspace_dir
         .as_deref()
         .unwrap_or_else(|| config.modules_dir_anchor().unwrap_or_else(|| Path::new(".")));
@@ -187,6 +182,23 @@ pub(super) fn apply_existing_patch_file(
         .map_err(PatchError::ApplyExistingPatch)
 }
 
+/// The patch file configured for `target`, if any. `patch-commit` keys the
+/// patch of a git-hosted package by its version, while the target's bare
+/// specifier is the package's tarball URL, so both are tried.
+pub(super) fn find_existing_patch_file<'a>(
+    patched_dependencies: &'a IndexMap<String, String>,
+    target: &PatchTarget,
+) -> Option<&'a String> {
+    [&target.bare_specifier, &target.version]
+        .into_iter()
+        .find_map(|specifier| patched_dependencies.get(&format!("{}@{specifier}", target.alias)))
+        .or_else(|| {
+            target.apply_to_all
+                .then(|| patched_dependencies.get(&target.alias))
+                .flatten()
+        })
+}
+
 struct ExistingPatchFileContext {
     project_root: PathBuf,
     patches_dir: PathBuf,

pnpm/crates/cli/src/cli_args/patch/tests.rs

@@ -5,7 +5,8 @@ use super::{
 };
 #[cfg(unix)]
 use crate::cli_args::patch::paths::checked_existing_patch_file_path;
-use crate::cli_args::patch::paths::default_edit_dir_name;
+use crate::cli_args::patch::paths::{default_edit_dir_name, find_existing_patch_file};
+use indexmap::IndexMap;
 use std::{io::IsTerminal, path::Path};
 use tempfile::tempdir;
 
@@ -223,6 +224,27 @@ fn default_edit_dir_name_falls_back_to_alias_then_requested_package() {
     assert_eq!(default_edit_dir_name("chalk@npm:chalk@5.3.0", &target), "chalk@npm:chalk@5.3.0");
 }
 
+/// Regression test for <https://github.com/pnpm/pnpm/issues/9699>.
+#[test]
+fn existing_patch_file_of_a_git_hosted_package_is_found_by_version() {
+    let tarball = "https://codeload.github.com/example/hi/tar.gz/deadbeef";
+    let target = PatchTarget {
+        alias: "hi".to_string(),
+        version: "1.0.0".to_string(),
+        bare_specifier: tarball.to_string(),
+        apply_to_all: false,
+        git_tarball_url: Some(tarball.to_string()),
+        package_key: format!("hi@{tarball}").parse().expect("package key"),
+    };
+    let patched_dependencies =
+        IndexMap::from([("hi@1.0.0".to_string(), "patches/hi@1.0.0.patch".to_string())]);
+
+    assert_eq!(
+        find_existing_patch_file(&patched_dependencies, &target).map(String::as_str),
+        Some("patches/hi@1.0.0.patch"),
+    );
+}
+
 struct FakePrompt {
     selected: usize,
     apply_to_all: bool,

pnpm11/patching/commands/src/getPatchedDependency.ts

@@ -13,7 +13,14 @@ export type GetPatchedDependencyOptions = {
   lockfileDir: string
 } & Pick<Config, 'virtualStoreDir' | 'modulesDir'>
 
-export type GetPatchedDependencyResult = ParseWantedDependencyResult & { applyToAll: boolean }
+export type GetPatchedDependencyResult = ParseWantedDependencyResult & {
+  applyToAll: boolean
+  /**
+   * The installed version of the chosen package. It differs from `bareSpecifier`
+   * when the package is git-hosted, in which case `bareSpecifier` is its tarball URL.
+   */
+  version?: string
+}
 
 export async function getPatchedDependency (rawDependency: string, opts: GetPatchedDependencyOptions): Promise<GetPatchedDependencyResult> {
   const dep = parseWantedDependency(rawDependency)
@@ -29,10 +36,10 @@ export async function getPatchedDependency (rawDependency: string, opts: GetPatc
 
   dep.alias = dep.alias ?? rawDependency
   if (preferredVersions.length > 1) {
-    let version: string
+    let bareSpecifier: string
     let applyToAll: boolean
     try {
-      version = await select({
+      bareSpecifier = await select({
         message: 'Choose which version to patch',
         choices: preferredVersions.map(preferred => ({
           name: preferred.version,
@@ -53,7 +60,8 @@ export async function getPatchedDependency (rawDependency: string, opts: GetPatc
     return {
       ...dep,
       applyToAll,
-      bareSpecifier: version,
+      bareSpecifier,
+      version: preferredVersions.find(preferred => (preferred.gitTarballUrl ?? preferred.version) === bareSpecifier)?.version,
     }
   } else {
     const preferred = preferredVersions[0]
@@ -62,12 +70,14 @@ export async function getPatchedDependency (rawDependency: string, opts: GetPatc
         ...dep,
         applyToAll: false,
         bareSpecifier: preferred.gitTarballUrl,
+        version: preferred.version,
       }
     }
     return {
       ...dep,
       applyToAll: !dep.bareSpecifier,
       bareSpecifier: preferred.version,
+      version: preferred.version,
     }
   }
 }

pnpm11/patching/commands/src/patch.ts

@@ -133,7 +133,7 @@ To commit your changes, run:
 
 function tryPatchWithExistingPatchFile (
   {
-    patchedDep: { applyToAll, alias, bareSpecifier },
+    patchedDep: { applyToAll, alias, bareSpecifier, version },
     patchedDir,
     patchedDependencies,
     lockfileDir,
@@ -149,6 +149,9 @@ function tryPatchWithExistingPatchFile (
   if (bareSpecifier) {
     existingPatchFile = patchedDependencies[`${alias}@${bareSpecifier}`]
   }
+  if (!existingPatchFile && version) {
+    existingPatchFile = patchedDependencies[`${alias}@${version}`]
+  }
   if (!existingPatchFile && applyToAll) {
     existingPatchFile = patchedDependencies[alias]
   }

pnpm11/patching/commands/test/patch.test.ts

@@ -1518,6 +1518,15 @@ describe('patch and commit in workspaces', () => {
     expect(patchContent).toContain('diff --git')
     expect(patchContent).toContain('// test patching')
     expect(fs.readFileSync('./project-2/node_modules/hi/index.js', 'utf8')).toContain('// test patching')
+
+    // re-patch
+    fs.rmSync(patchDir, { recursive: true })
+    const repatchOutput = await patch.handler({
+      ...defaultPatchOption,
+      patchedDependencies: workspaceManifest!.patchedDependencies,
+    }, ['hi'])
+    const repatchDir = getPatchDirFromPatchOutput(repatchOutput)
+    expect(fs.readFileSync(path.join(repatchDir, 'index.js'), 'utf8')).toContain('// test patching')
   })
 })