Never read or rewrite project files outside the git repository root

crates/socket-patch-cli/CLI_CONTRACT.md

@@ -661,7 +661,9 @@ are patched by `socket-patch apply` like every other ecosystem:
   --check` is a read-only audit of the committed redirect.
   The `go.work` in effect is resolved as go resolves it: `GOWORK` naming an absolute file, none under
   `GOWORK=off`, else (unset, empty or `auto`) the nearest `go.work` at or above the project; a relative
-  `GOWORK` is invalid to go, so nothing is written or attested. A `-modfile` in `GOFLAGS` (#1799)
+  `GOWORK` is invalid to go, so nothing is written or attested. A `go.work` outside the repository
+  root is never read and refuses the same way (see "Reads bounded to the repository root").
+  A `-modfile` in `GOFLAGS` (#1799)
   that names any file other than the project's `go.mod` (a relative one is taken from the project
   directory) makes go build from that file and ignore `go.mod`'s replaces, and in workspace mode go
   refuses `-modfile` outright: `apply`, `vendor` and `scan --mode hosted` write nothing
@@ -903,6 +905,19 @@ socket-patch creates `.socket/` and everything under it itself and never writes
 
 Not covered: the agent-mode blob cache and manifest are checked from `.socket` down, so a `.socket` that is itself a link still redirects those writes (deciding that at lock time is deferred).
 
+### Reads bounded to the repository root
+
+**Workspace runs only.** The bound applies to project-scoped runs (the default `--cwd` project). A global run (`--global` / `-g`, or `--global-prefix`, on any command) reads anywhere on the system, so it can scan global `node_modules`, `site-packages`, `~/.m2`, the cargo and Go caches, and their settings wherever they live: nothing in this section applies to it. The mode is fixed once per run from those flags and passed to every bounded read (core `utils::repo_root::ReadScope`: `Workspace` or `Global`; `ReadBoundary::Workspace { root }` or `ReadBoundary::Unbounded`). It is never inferred from the filesystem. Hosted and vendored mode refuse global runs anyway, and VEX discovery and verification do not run in them.
+
+VEX discovery, the lock inventory, hosted mode and vendored mode never read a PROJECT file outside the repository root: the git checkout enclosing the project (the nearest `.git`, by the same rules as the repository lookup), or the project directory itself when there is none. One check (core `utils::repo_root::ReadBoundary`) decides it on the REAL path: every project-file read is checked, an in-tree name included, and a level that resolves outside through `..` or a symlink (a `..` after a link climbs from the link's target, as the OS resolves it) counts as outside. A refused read behaves like a missing file to a reader; a writer refuses with the reason (`… is outside the repository root …; socket-patch does not read project files outside it`). Machine-level tool configuration (the user `~/.npmrc` / `.yarnrc.yml` / `NuGet.Config`, the `GOENV` file, `$CARGO_HOME`, module and package caches) is not a project file and is read as before.
+
+- **Go** (an upward lookup: without a checkout, as before): a `go.work` outside the root (an ancestor's, or one an absolute `GOWORK` names) is only noticed, never read: the workspace is invalid, so vendored and hosted writes refuse with the Go workspace refusal and discovery withholds every Go ref. Inside the root, a `use` member or a `replace` directory outside it reads as missing, so the selection it would decide is unknown.
+- **Requirements includes**: a `-r` include outside the root is never read. Discovery and the lock inventory see it as missing; vendored mode refuses `pypi_requirements_outside_root`, since the pins pip installs from it are unknowable.
+- **NuGet parent configs** (an upward lookup: without a checkout, as before): a `nuget.config` in a directory above the root is never read. Vendoring refuses (`… also merges <path>, which is outside the repository root …`) and hosted mode skips each NuGet dep with `redirect_nuget_inherited_config_outside_root`, writing nothing for it.
+- **Relative and absolute references read through the project view** (yarn `file:` / `portal:` / `link:` copies, include chains, any `../` path a lockfile names) and the hosted upstream restore's staged reads: outside the root they read as missing, and the restore refuses.
+- **Upward lookups** (a workspace root or settings file the package manager searches the project's ancestors for): inside a git checkout none reads above the repository root. When one of the files the lookup would read exists above it (a stat, never a read, and never in the home directory or above), the tool may honor it, so writers refuse and readers withhold: a lockless npm-family member or a member's own npm/Bun/vlt lock under a `package.json`, `pnpm-workspace.yaml` or `vlt.json` above (`redirect_workspace_lockfile_elsewhere` in hosted mode, `vendor_lockfile_missing` in vendored mode, unattested in discovery); the nearest `pnpm-workspace.yaml` above (but never one in the home directory or above it) counts as governing (`redirect_pnpm_settings_elsewhere`, `vendor_pnpm_settings_elsewhere`, and a `gitBranchLockfile` that may be on); a uv workspace `pyproject.toml` above (`redirect_workspace_lockfile_elsewhere`, `pypi_uv_workspace_unsupported`) or uv settings above (`pypi_uv_ancestor_settings`; hosted `redirect_uv_project_unsupported` / `redirect_uv_script_unsupported` / `redirect_uv_lock_unsupported`); a `Cargo.toml` above (`cargo_manifest_not_workspace_root`) or a `.cargo/config(.toml)` above (`user_authored_patch_entry` in vendored mode; hosted mode refuses the run with `redirect_cargo_config_outside_root`; agent-mode `apply` and `apply --check` refuse a run with Cargo patches with `cargo_config_outside_root`, naming the file, since it may replace crates.io while apply would patch the registry cache, and the cargo build-cache invalidation warns `cargo_build_cache_stale` that a `build.target-dir` / `build.build-dir` set there was not read); a `.yarnrc.yml` above (its `nodeLinker` reads as unknown, so PnP; no `pnpmStoreFolder` store is admitted; the Berry upstream restore refuses the registry lookup); a yarn classic `.yarnrc` / `.npmrc` above, or a workspace member linked from outside the repository (`redirect_yarn_classic_offline_mirror`, naming the file or member); a `pom.xml`, Gradle settings or `build.sbt` above (`not_build_root`). Gradle settings above are not analysed by the crawler, an `injectEnvironmentFiles` dotenv file outside the repository (other than beside the home rc) injects nothing, a cargo `[patch]` path outside it reads as unknown (`user_authored_patch_entry`), and agent mode's build-cache invalidation stays inside it. Without a git checkout every upward lookup walks on as before.
+- **Vendored ownership**: writers, reverters and the GC claim a lockfile reference only when it is root-anchored into THIS project's `.socket/vendor/` (`./.socket/vendor/…`, or `../` from a file below the root back to exactly the root). A sibling checkout's `../.socket/vendor/<eco>/<uuid>/…`, even for the same patch uuid, is never rewritten, reverted or deleted; the revert leaves it with `vendor_lock_entry_drifted` and keeps the artifact. The one exception is pnpm <= 8, which records override specifiers as machine-absolute paths itself: an absolute `…/.socket/vendor/npm/<uuid>/<leaf>` naming the entry's own uuid and leaf is still the entry's.
+
 ## Vendor command contract
 
 `vendor` converts the hosted patches pinned in the project's lockfiles into committable

crates/socket-patch-cli/src/args.rs

@@ -447,6 +447,14 @@ impl GlobalArgs {
         self.global || self.global_prefix.is_some()
     }
 
+    /// The read scope this run's mode fixes for every bounded read: a
+    /// global run (`--global` / `--global-prefix`) reads anywhere on the
+    /// system; a project run never reads a project file outside the
+    /// repository root (see `socket_patch_core::utils::repo_root`).
+    pub(crate) fn read_scope(&self) -> socket_patch_core::utils::repo_root::ReadScope {
+        socket_patch_core::utils::repo_root::ReadScope::of_global(self.is_global())
+    }
+
     /// Whether `--ecosystems` selects `eco` (every ecosystem when unset or
     /// empty). The names are validated at parse time, so this is an exact
     /// match.

crates/socket-patch-cli/src/commands/apply.rs

@@ -471,13 +471,17 @@ async fn run_check(args: &ApplyArgs, manifest_path: &Path) -> i32 {
     // The same PnP gate `apply` runs: a PnP tree hides every npm copy, so
     // without it each npm patch would read as not installed and pass calm.
     if matches!(
-        detect_npm_pkg_manager(&args.common.cwd),
+        detect_npm_pkg_manager(args.common.read_scope(), &args.common.cwd),
         NpmPkgManager::YarnBerryPnP
     ) && eco_in_local_scope(&args.common, Ecosystem::Npm)
         && manifest_targets_npm(&tree)
     {
         return refuse_yarn_pnp(args);
     }
+    // The same cargo gate `apply` runs (see [`cargo_config_outside_root`]).
+    if let Some(why) = cargo_config_outside_root(args, &tree) {
+        return refuse_cargo_config_outside_root(args, &why, &[]);
+    }
     let mut in_sync: Vec<String> = Vec::new();
     let mut not_installed: Vec<String> = Vec::new();
     if !tree.patches.is_empty() {
@@ -948,6 +952,52 @@ pub(crate) fn result_to_event(result: &ApplyResult, dry_run: bool) -> PatchEvent
 /// True when the manifest records at least one npm patch — the only kind a
 /// PnP layout can block (a polyglot repo's pypi/gem/go patches live outside
 /// `node_modules` and apply fine).
+/// The refusal code of [`cargo_config_outside_root`].
+const CARGO_CONFIG_OUTSIDE_ROOT: &str = "cargo_config_outside_root";
+
+/// Why a workspace apply cannot patch this project's Cargo crates: a
+/// `.cargo/config` / `config.toml` sits above the repository root (stat
+/// only; it is never read), and cargo merges it into the build, so it may
+/// replace crates.io with another source while apply patches the shared
+/// registry cache. `None` for a global run, a run without Cargo patches
+/// or a project that is no Cargo project.
+fn cargo_config_outside_root(args: &ApplyArgs, manifest: &PatchManifest) -> Option<String> {
+    let cwd = &args.common.cwd;
+    if !eco_in_local_scope(&args.common, Ecosystem::Cargo)
+        || !manifest
+            .patches
+            .keys()
+            .any(|p| Ecosystem::from_purl(p) == Some(Ecosystem::Cargo))
+        || !(cwd.join("Cargo.toml").is_file() || cwd.join("Cargo.lock").is_file())
+    {
+        return None;
+    }
+    socket_patch_core::vendor::cargo_config::config_above_repo(cwd).map(|why| {
+        format!(
+            "{why}: it may replace crates.io with another source, so the registry copy apply \
+             patches may not be what cargo builds; move the settings into the repository's \
+             .cargo/config.toml (or run with --global to patch the registry cache anyway)"
+        )
+    })
+}
+
+/// Print the [`cargo_config_outside_root`] refusal and return the exit
+/// code.
+fn refuse_cargo_config_outside_root(args: &ApplyArgs, why: &str, skipped: &[PatchEvent]) -> i32 {
+    if args.common.json {
+        let mut env = Envelope::new(Command::Apply);
+        env.dry_run = args.common.dry_run;
+        for skip in skipped {
+            env.record(skip.clone());
+        }
+        env.mark_error(EnvelopeError::new(CARGO_CONFIG_OUTSIDE_ROOT, why));
+        println!("{}", env.to_pretty_json());
+    } else {
+        eprintln!("Error: {why}");
+    }
+    1
+}
+
 fn manifest_targets_npm(manifest: &PatchManifest) -> bool {
     manifest
         .patches
@@ -1061,7 +1111,7 @@ pub async fn run(args: ApplyArgs) -> i32 {
         // filter excluding npm never touches it.
         if eco_in_local_scope(&args.common, Ecosystem::Npm)
             && matches!(
-                detect_npm_pkg_manager(&args.common.cwd),
+                detect_npm_pkg_manager(args.common.read_scope(), &args.common.cwd),
                 NpmPkgManager::YarnBerryPnP
             )
         {
@@ -1388,7 +1438,17 @@ pub(crate) async fn run_locked(
     // informational note; the substantive safety is core's rename-over
     // write (`utils::fs::atomic_write_bytes` never touches the store's
     // shared inode).
-    match detect_npm_pkg_manager(&args.common.cwd) {
+    // A cargo config above the repository root is never read in a
+    // workspace run; it may move crates.io elsewhere, so the Cargo patches
+    // refuse instead of patching the registry cache blind.
+    if let Some(why) = cargo_config_outside_root(&args, &manifest) {
+        let code = refuse_cargo_config_outside_root(&args, &why, &user_patch_skips);
+        return ApplyRunReport {
+            skipped: user_patch_skips,
+            ..ApplyRunReport::run_failure(code, CARGO_CONFIG_OUTSIDE_ROOT, why)
+        };
+    }
+    match detect_npm_pkg_manager(args.common.read_scope(), &args.common.cwd) {
         NpmPkgManager::YarnBerryPnP => {
             if eco_in_local_scope(&args.common, Ecosystem::Npm) && manifest_targets_npm(&manifest) {
                 let code = refuse_yarn_pnp_with_skips(&args, &user_patch_skips);
@@ -1512,6 +1572,7 @@ pub(crate) async fn run_locked(
                 });
                 cache_warnings.extend(
                     socket_patch_core::utils::cargo_build_cache::invalidate_project(
+                        args.common.read_scope(),
                         &args.common.cwd,
                         rewritten.map(|r| r.package_key.as_str()),
                     )
@@ -2712,6 +2773,7 @@ async fn apply_patches_inner(
                     // extension, or is refused with nothing written (#1996).
                     let result = if Ecosystem::from_purl(purl) == Some(Ecosystem::Gem) {
                         let applied = gem_ext::apply_gem_package_patch(
+                            args.common.read_scope(),
                             variant_purl,
                             pkg_path,
                             &patch.files,
@@ -2735,6 +2797,7 @@ async fn apply_patches_inner(
                         applied.result
                     } else {
                         apply_package_patch(
+                            args.common.read_scope(),
                             variant_purl,
                             pkg_path,
                             &patch.files,
@@ -2892,6 +2955,7 @@ async fn apply_patches_inner(
                         }
                         None => {
                             apply_package_patch(
+                                args.common.read_scope(),
                                 purl,
                                 pkg_path,
                                 &patch.files,
@@ -3423,6 +3487,7 @@ async fn apply_maven_base(m: &MavenBase<'_>) -> MavenApplied {
                 }
                 attempted = true;
                 let mut result = apply_package_patch(
+                    args.common.read_scope(),
                     variant,
                     &dir,
                     &files,
@@ -3443,6 +3508,7 @@ async fn apply_maven_base(m: &MavenBase<'_>) -> MavenApplied {
             if copy_attempted && !absent.is_empty() {
                 attempted = true;
                 let result = apply_package_patch(
+                    args.common.read_scope(),
                     variant,
                     copy,
                     &absent,
@@ -3743,6 +3809,58 @@ mod tests {
         AppliedVia as CoreAppliedVia, ApplyResult, VerifyResult, VerifyStatus,
     };
 
+    /// Review finding 3: a workspace apply of Cargo patches refuses when a
+    /// `.cargo/config.toml` above the repository root (never read) may
+    /// replace crates.io; a global run, or one without it, does not.
+    #[test]
+    fn cargo_patches_refuse_under_a_cargo_config_above_the_repository() {
+        #[derive(clap::Parser)]
+        struct Wrap {
+            #[command(flatten)]
+            args: ApplyArgs,
+        }
+        let tmp = tempfile::tempdir().unwrap();
+        let outer = std::fs::canonicalize(tmp.path()).unwrap();
+        let app = outer.join("repo");
+        std::fs::create_dir_all(app.join(".git")).unwrap();
+        std::fs::write(app.join("Cargo.toml"), "[package]\nname = \"app\"\n").unwrap();
+        let record: socket_patch_core::manifest::schema::PatchRecord =
+            serde_json::from_value(serde_json::json!({
+                "uuid": "11111111-1111-4111-8111-111111111111",
+                "exportedAt": "",
+                "files": {},
+                "vulnerabilities": {},
+                "description": "",
+                "license": "",
+                "tier": "free",
+            }))
+            .unwrap();
+        let mut manifest = PatchManifest::default();
+        manifest
+            .patches
+            .insert("pkg:cargo/serde@1.0.0".to_string(), record);
+        let parse = |extra: &[&str]| {
+            let cwd = app.display().to_string();
+            let mut argv = vec!["t", "--cwd", cwd.as_str()];
+            argv.extend_from_slice(extra);
+            <Wrap as clap::Parser>::try_parse_from(argv).unwrap().args
+        };
+        assert_eq!(cargo_config_outside_root(&parse(&[]), &manifest), None);
+        std::fs::create_dir_all(outer.join(".cargo")).unwrap();
+        std::fs::write(
+            outer.join(".cargo/config.toml"),
+            "[source.crates-io]\nreplace-with = \"v\"\n[source.v]\ndirectory = \"vendor\"\n",
+        )
+        .unwrap();
+        let why = cargo_config_outside_root(&parse(&[]), &manifest).unwrap();
+        assert!(why.contains(".cargo/config.toml"), "{why}");
+        assert!(why.contains("outside the repository"), "{why}");
+        assert_eq!(
+            cargo_config_outside_root(&parse(&["--global"]), &manifest),
+            None
+        );
+    }
+
     /// A new-file collision's empty expected hash reads `(new file)` in the
     /// verbose summary; a real hash is shown as is.
     #[test]

crates/socket-patch-cli/src/commands/rollback.rs

@@ -3069,6 +3069,7 @@ pub(crate) async fn rollback_patches_inner(
                 for path in &found {
                     for copy in
                         socket_patch_core::crawlers::npm_crawler::find_store_peer_variant_copies(
+                            common.read_scope(),
                             path,
                         )
                         .await
@@ -3277,6 +3278,7 @@ pub(crate) async fn rollback_patches_inner(
                 Some(r) => r,
                 None => {
                     let mut result = rollback_package_patch(
+                        common.read_scope(),
                         purl,
                         pkg_path,
                         &patch.files,
@@ -3318,6 +3320,7 @@ pub(crate) async fn rollback_patches_inner(
             // isolated-store entry, #1084) is restored here, or fails the
             // run and keeps the record, before the record is dropped.
             match socket_patch_core::patch::rollback::rollback_store_copies_holding_patch(
+                common.read_scope(),
                 purl,
                 pkg_path,
                 files,
@@ -3400,6 +3403,7 @@ pub(crate) async fn rollback_patches_inner(
     if !common.dry_run {
         warnings.extend(
             socket_patch_core::utils::cargo_build_cache::invalidate_project(
+                common.read_scope(),
                 &common.cwd,
                 results
                     .iter()
@@ -3817,8 +3821,15 @@ async fn rollback_maven_target(
             }
         }
     }
-    let mut result =
-        rollback_package_patch(&target.purl, &target.dir, files, blobs_path, common.dry_run).await;
+    let mut result = rollback_package_patch(
+        common.read_scope(),
+        &target.purl,
+        &target.dir,
+        files,
+        blobs_path,
+        common.dry_run,
+    )
+    .await;
     if !result.success || common.dry_run {
         return result;
     }

crates/socket-patch-cli/src/commands/scan/discovery.rs

@@ -614,7 +614,7 @@ pub(crate) async fn nested_project_skips(
     // keeps the package the root's, whatever copy the crawl kept.
     // An unreadable tree keeps every candidate the root's (the backend
     // then reports it), rather than dropping a package the root installs.
-    let crawler = socket_patch_core::crawlers::NpmCrawler::new();
+    let crawler = socket_patch_core::crawlers::NpmCrawler::for_options(options);
     let wanted: Vec<String> = candidates.keys().cloned().collect();
     let Ok(nm_roots) = crawler.get_node_modules_paths(options).await else {
         return Default::default();