Fix Hatch environments being invisible to stale-install checks and VEX (#335)

crates/socket-patch-cli/CLI_CONTRACT.md

@@ -189,7 +189,7 @@ The hidden alias `--no-apply` on `get --save-only` is **part of the contract** 
 
 `repair` keeps its `gc` visible alias.
 
-**Python stale-install guard**: after a hosted redirect, `scan` / `get` use the Python crawler to inspect every matching installed package, including Poetry's out-of-tree virtualenvs and `--global-prefix`. A readable file that differs from the patch's `afterHash` emits `redirect_pypi_stale_install` in JSON `redirect.warnings[]` and human stderr. The probe changes no installed files, re-runs on idempotent scans, and falls back to persisted patch records when fresh record fetching fails. Missing/unreadable files alone do not prove staleness; lock-only checkouts stay quiet. Dry runs skip the probe. Same-run VEX excludes positively stale Python packages (qualifier-insensitive), even with `--vex-no-verify` or a healthy copy in another interpreter; if nothing remains to attest, the command exits 1 with `no_applicable_patches`. Reinstall from the rewritten lock in the affected interpreter and verify with `socket-patch vex`.
+**Python stale-install guard**: after a hosted redirect, `scan` / `get` use the Python crawler to inspect every matching installed package, including Poetry's out-of-tree virtualenvs, the project's Hatch environments (Hatch's data dir / `HATCH_DATA_DIR`, `[dirs.env] virtual`, explicit env `path`s) and `--global-prefix`. A readable file that differs from the patch's `afterHash` emits `redirect_pypi_stale_install` in JSON `redirect.warnings[]` and human stderr. The probe changes no installed files, re-runs on idempotent scans, and falls back to persisted patch records when fresh record fetching fails. Missing/unreadable files alone do not prove staleness; lock-only checkouts stay quiet. Dry runs skip the probe. Same-run VEX excludes positively stale Python packages (qualifier-insensitive), even with `--vex-no-verify` or a healthy copy in another interpreter; if nothing remains to attest, the command exits 1 with `no_applicable_patches`. Reinstall from the rewritten lock in the affected interpreter and verify with `socket-patch vex`. A stale Hatch environment instead names `hatch env remove <env>` / `hatch env prune`: Hatch's pip installer (and uv before Hatch 1.16) keeps a same-version release, so only a recreated env picks up the patch. The same Hatch envs are what agent mode patches and `vex` judges for a Hatch project.
 
 ### socket.yml patch policy (v5.0)
 
@@ -327,7 +327,7 @@ Contract details:
 * **JSON success surface**: `apply` adds a top-level `vex` object to its envelope; `scan` adds a top-level `vex` key to its result. Both carry `{ path, statements, format: "openvex-0.2.0" }`.
 * `apply`'s no-manifest early exit (the `noManifest` success no-op; v5.0: its human line is `No patch manifest found; nothing to apply.` — it names the missing `.socket/manifest.json`, not the folder, since `.socket/` may legitimately hold vendored state) and `vendor`'s (`No manifest found, nothing to vendor.` — a project with hosted pins ejects instead, v5.0) still generate the document from the lockfiles and the vendor ledger (manifest-less VEX: hosted / vendored checkouts carry no manifest). Nothing referenced anywhere keeps the calm exit 0 (a stale document at the path is removed; `--json` carries any discovery diagnostics in `warnings[]`); any other VEX failure fails the command with exit 1 — including a run whose only candidates are omitted `record_unavailable` (an `--offline` run over a lockfile-wired checkout with no local records), so an ambient `SOCKET_VEX` there fails the install. `--dry-run` skips generation on both, and so does `apply --check` — it stays read-only and offline-safe, leaving the output path untouched. `scan` has no such early exit: with no manifest and nothing wired anywhere its `--vex` fails with `manifest_not_found`.
 * **Stale-doc removal (v3.5)**: a run that ends in a VEX error removes a recognizably-OpenVEX file (JSON whose `@context` names openvex.dev) already sitting at the output path — a pipeline reusing one path can never ship yesterday's attestation for a now-unpatched tree. Unrelated files at the path are never touched; a mid-write partial that no longer parses as JSON is left for downstream parsers to reject loudly.
-* **Additive warnings (v3.5)**: `product_not_iri` (the `--product`/`--vex-product` override is neither a `pkg:` purl nor an absolute IRI; honored verbatim, warned) and `vendored_tree_out_of_sync` (a healthy vendored attestation stands on the committed artifact + lock wiring while the PRESENT installed tree hash-mismatches the patched bytes — run the package manager's install; the attestation itself is unchanged). Both ride stderr in human mode and `warnings[]` in the standalone `vex --json` envelope. Same channel for `product_multiple_manifests` (auto-detect found several project manifests and names the one it used), `vex_stale_doc_removed` (the stale-doc removal above happened), the manifest-less plan's advisories — `vex_wiring_conflict` (the lockfiles wire a package to different patches: which files, which uuids, how to fix it), `vex_record_superseded` (a recorded patch replaced by the lockfile-wired one), `vex_claim_unwired` (a ledger claim whose patch the lockfiles still mention, but not as wiring), `vex_record_offline` / `vex_record_not_found` / `vex_record_fetch_failed` (why a lockfile-wired patch has no record — the detail behind a `record_unavailable` skip) and `api_auth_fallback` (the authenticated API refused the credentials and the public proxy served free patches only; `get` / `scan`'s warning text) — and, standalone only, `org_looks_like_path` (`-o`/`--org` given a file-shaped value — `-O` is `--output`). The standalone error envelope carries `warnings[]` too. An embedded `--vex` that fails also folds each omitted patch into the host command's `warnings[]` as `vex_omitted` (`<purl>: <why> (<errorCode>)` — standalone `vex` lists them as `skipped` events), and `--silent` lists them as `omitted: <purl> (<errorCode>)` lines under the error. A corrupt `.socket/vendor/state.json` is no longer degraded with a warning: every form of vex fails with `vendor_ledger_corrupt` (see the error-code table). A malformed pre-v5 `redirect-state.json` is, as of v5.0, only the `redirect_ledger_corrupt` warning (hosted mode keeps no ledger; the file is an optional migration record source).
+* **Additive warnings (v3.5)**: `product_not_iri` (the `--product`/`--vex-product` override is neither a `pkg:` purl nor an absolute IRI; honored verbatim, warned) and `vendored_tree_out_of_sync` (a healthy vendored attestation stands on the committed artifact + lock wiring while the PRESENT installed tree hash-mismatches the patched bytes — run the package manager's install (for a project with Hatch environments the detail also names `hatch env remove <env>`, since Hatch keeps an installed release); the attestation itself is unchanged). Both ride stderr in human mode and `warnings[]` in the standalone `vex --json` envelope. Same channel for `product_multiple_manifests` (auto-detect found several project manifests and names the one it used), `vex_stale_doc_removed` (the stale-doc removal above happened), the manifest-less plan's advisories — `vex_wiring_conflict` (the lockfiles wire a package to different patches: which files, which uuids, how to fix it), `vex_record_superseded` (a recorded patch replaced by the lockfile-wired one), `vex_claim_unwired` (a ledger claim whose patch the lockfiles still mention, but not as wiring), `vex_record_offline` / `vex_record_not_found` / `vex_record_fetch_failed` (why a lockfile-wired patch has no record — the detail behind a `record_unavailable` skip) and `api_auth_fallback` (the authenticated API refused the credentials and the public proxy served free patches only; `get` / `scan`'s warning text) — and, standalone only, `org_looks_like_path` (`-o`/`--org` given a file-shaped value — `-O` is `--output`). The standalone error envelope carries `warnings[]` too. An embedded `--vex` that fails also folds each omitted patch into the host command's `warnings[]` as `vex_omitted` (`<purl>: <why> (<errorCode>)` — standalone `vex` lists them as `skipped` events), and `--silent` lists them as `omitted: <purl> (<errorCode>)` lines under the error. A corrupt `.socket/vendor/state.json` is no longer degraded with a warning: every form of vex fails with `vendor_ledger_corrupt` (see the error-code table). A malformed pre-v5 `redirect-state.json` is, as of v5.0, only the `redirect_ledger_corrupt` warning (hosted mode keeps no ledger; the file is an optional migration record source).
 
 ### VEX provenance markers (contract)
 
@@ -1234,6 +1234,7 @@ Every `--json` invocation emits a single JSON object that follows the **unified
 | `pypi_poetry_symlink_unsupported` / `pypi_pipenv_symlink_unsupported` / `pypi_requirements_symlink_unsupported` | `failed` | vendor (pypi, v5.0): a target file (`pyproject.toml` / `poetry.lock`, `Pipfile` / `Pipfile.lock`, or any planned `requirements*.txt`) is a symlink — refused before any write on wire AND on revert (the revert keeps the artifact, `kept_artifact`); the twins of the existing pdm/uv symlink refusals. |
 | `pypi_poetry_changed` / `pypi_pdm_changed` / `pypi_pipenv_changed` / `pypi_uv_changed` | `failed` | vendor (pypi, v5.0): the lock / project file changed between the read that planned the edit and the first write — refused before any write (worded like `pypi_lock_changed`: "<file> changed during vendoring; re-run"). |
 | `pypi_pipenv_stale_install` | `skipped` (warning) | vendor (pipenv): the vendored twin of `redirect_pypi_stale_install` — the project's venv still holds the upstream release Pipenv will not reinstall over; the detail names the `pipenv run pip uninstall -y <pkg> && pipenv sync` remedy. |
+| `pypi_hatch_stale_install` | `skipped` (warning) | vendor (hatch): an existing Hatch environment of the project (found under Hatch's data dir, `dirs.env.virtual` or an explicit env `path`) still holds the upstream release; Hatch keeps it on the next `hatch run`, so the detail names the env and the `hatch env remove <env>` / `hatch env prune` remedy. |
 | `pypi_pipenv_installer_unknown` | `skipped` (warning) | vendor (pipenv): no `pipenv` answered on PATH; the vendored references assume Pipenv 2018 or later (7–11 cannot consume them — use hosted mode there); `SOCKET_PIPENV_MAJOR` pins the release. |
 | `vendor_lock_entry_relocked` | revert `warnings[]` | vendor `--revert` / rollback (pipenv): a relock regenerated the wired entry to a registry reference, or removed it; the record is retired (artifact removed, ledger entry dropped) instead of drift-kept. |
 | `pypi_{poetry,pdm,pipenv}_no_lockfile` | `failed` | vendor (pypi): a lock-less tool marker with no `requirements.txt` fallback — run `<tool> lock`. |

crates/socket-patch-cli/src/commands/scan/hosted/python.rs

@@ -44,6 +44,13 @@ pub(super) async fn stale_install_warnings(
     // fallback to the global interpreters would judge an unrelated Python's
     // copy of the release (a tool venv on PATH) and warn falsely.
     // --global / --global-prefix keep their meaning.
+    // Hatch envs need their own remedy: a reinstall from the rewritten
+    // pyproject does nothing there (#335).
+    let hatch_envs = if common.is_global() {
+        Vec::new()
+    } else {
+        socket_patch_core::crawlers::hatch_env::hatch_environments(&common.cwd).await
+    };
     let paths = if common.is_global() {
         crawler
             .get_site_packages_paths(&common.crawler_options())
@@ -105,7 +112,11 @@ pub(super) async fn stale_install_warnings(
             // (`install`, `install --deploy`, `sync` all keep the installed
             // bytes on every major), and `pipenv uninstall` rewrites the
             // Pipfile and re-locks the patch away — name the verified remedy.
-            let remedy = if pipenv_purls.contains(&purl) {
+            let hatch_env =
+                socket_patch_core::crawlers::hatch_env::environment_of(&hatch_envs, &site);
+            let remedy = if let Some(env) = hatch_env {
+                socket_patch_core::crawlers::hatch_env::stale_install_remedy(&env.name)
+            } else if pipenv_purls.contains(&purl) {
                 let name = strip_purl_qualifiers(&purl)
                     .strip_prefix("pkg:pypi/")
                     .and_then(|rest| rest.split('@').next())
@@ -214,6 +225,55 @@ mod tests {
         assert!(out.warnings.is_empty());
     }
 
+    /// #335: a Hatch env keeps the upstream release after the rewrite, and
+    /// the probe must find it (Hatch keeps envs out of `./.venv`) and name
+    /// Hatch's remedy, not "reinstall from the rewritten lock".
+    #[tokio::test]
+    async fn hatch_env_gets_the_stale_install_warning_with_hatch_remedy() {
+        let tmp = tempfile::tempdir().unwrap();
+        let project = tmp.path().join("app");
+        std::fs::create_dir_all(&project).unwrap();
+        std::fs::write(
+            project.join("pyproject.toml"),
+            "[project]\nname = \"app\"\nversion = \"0.1.0\"\ndependencies = [\"six==1.16.0\"]\n\n[tool.hatch.envs.default]\npath = \"../hatch-envs/app\"\n",
+        )
+        .unwrap();
+        let env = tmp.path().join("hatch-envs").join("app");
+        std::fs::create_dir_all(&env).unwrap();
+        std::fs::write(env.join("pyvenv.cfg"), "home = /usr/bin\n").unwrap();
+        let site = if cfg!(windows) {
+            env.join("Lib").join("site-packages")
+        } else {
+            env.join("lib").join("python3.12").join("site-packages")
+        };
+        let dist = site.join("six-1.16.0.dist-info");
+        std::fs::create_dir_all(&dist).unwrap();
+        std::fs::write(dist.join("METADATA"), "Name: six\nVersion: 1.16.0\n").unwrap();
+        std::fs::write(site.join("six.py"), b"upstream").unwrap();
+
+        let common = crate::args::GlobalArgs {
+            cwd: project.clone(),
+            ..Default::default()
+        };
+        let purl = "pkg:pypi/six@1.16.0";
+        let confirmed = vec![(purl.to_string(), "six-uuid".to_string())];
+        let ledger = BTreeMap::from([("k".into(), record("six-uuid", "six.py", b"patched"))]);
+        let out = stale_install_warnings(&common, &confirmed, &BTreeSet::new(), &ledger).await;
+        assert_eq!(out.stale_purls, BTreeSet::from([purl.to_string()]));
+        assert_eq!(out.warnings.len(), 1);
+        let detail = out.warnings[0]["detail"].as_str().unwrap();
+        assert!(detail.contains("hatch env remove default"), "{detail}");
+        assert!(
+            !detail.contains("Reinstall from the rewritten lock"),
+            "{detail}"
+        );
+
+        // Patched in the env: nothing to warn about.
+        std::fs::write(site.join("six.py"), b"patched").unwrap();
+        let out = stale_install_warnings(&common, &confirmed, &BTreeSet::new(), &ledger).await;
+        assert!(out.warnings.is_empty());
+    }
+
     /// A legacy `.egg-info` install (pip < 23.1 building an sdist without
     /// `wheel`) is a real copy pip keeps on `install -r`, so the hosted
     /// stale-install guard must judge it like a `.dist-info` one (#447).

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

@@ -674,6 +674,26 @@ async fn generate_vex(
     // installed tree is present and running different bytes. Say so — a
     // build that bypasses the vendor wiring is unpatched until the next
     // package-manager install.
+    // A Hatch env is never resynced by an install: Hatch keeps a present
+    // release (#335), so name the remedy that recreates it.
+    let hatch_note = if outcome.vendored_out_of_sync.is_empty() || common.is_global() {
+        String::new()
+    } else {
+        match socket_patch_core::crawlers::hatch_env::hatch_environments(&common.cwd)
+            .await
+            .as_slice()
+        {
+            [] => String::new(),
+            envs => format!(
+                " A Hatch environment keeps an installed release on the next `hatch run`; \
+                 recreate it instead ({}).",
+                envs.iter()
+                    .map(|env| format!("`hatch env remove {}`", env.name))
+                    .collect::<Vec<_>>()
+                    .join(", ")
+            ),
+        }
+    };
     for purl in &outcome.vendored_out_of_sync {
         note_warning(
             warnings,
@@ -683,7 +703,7 @@ async fn generate_vex(
                 "{purl}: the installed tree does not match its vendored artifact; the \
                  attestation is based on the committed .socket/vendor artifact (the lockfile \
                  consumes it), but the live tree carries different bytes — re-run your \
-                 package manager's install to resync it."
+                 package manager's install to resync it.{hatch_note}"
             ),
         );
     }