v5: socket.yml patch rollout config and filtering

CHANGELOG.md

@@ -652,8 +652,57 @@ into the new version's section — see docs/releasing.md.
   batch is reported as failed (warning, or the all-failed error when it was
   the only batch) — instead of that one package being skipped silently.
 
+- **scan honors the repo's socket.yml.** `projectIgnorePaths` (the
+  scanner's key) now also keeps `scan` from patching the matching projects,
+  in every mode and in the in-memory engine, whether or not the file has a
+  `patches` block (malformed values there only warn
+  `socket_yml_ignored_value`). See "socket.yml patch policy" in
+  CLI_CONTRACT.md.
+- **Test and fixture trees are skipped by default when scan discovers
+  projects.** `test/ tests/ fixtures/ __fixtures__/ testdata/` (any case)
+  are built-in `ignorePaths` for discovered roots: hosted/vendored
+  PATH-glob matches (`scan 'services/*'`) and the in-memory engine's
+  detected roots (which used to skip them through a hard-coded, case-
+  sensitive segment list). A directory you name (`--cwd`, a literal PATH,
+  `projectRoots`) is not affected; `ignorePaths: ["!/e2e/tests/"]`
+  re-includes one, in memory too.
+- **An invalid socket.yml fails scan.** An unparseable file, a misspelled
+  top-level `patches` key (`Patches`, `patchs`), a top-level merge or
+  aliased key, an invalid `patches` block (unknown key, wrong type, bad glob, `patches`
+  without `version: 2`), or `socket.yml` and `socket.yaml` that disagree
+  now fail `scan` before any request or write: exit 1, `errorCode:
+  socket_yml_invalid` / `socket_yml_ambiguous`, the key path and the fix
+  in the message. `--no-socket-yml` ignores the file for one run.
+- **scan rejects a PATH outside the repository root** (exit 2): one socket.yml
+  policy per invocation.
+
 ### Added
 
+- **socket.yml patch policy (staged rollout).** A `patches` block in the
+  repo-root socket.yml narrows what `scan` patches: `enabled` (false =
+  report only), `includePaths` / `ignorePaths` (gitignore patterns matched
+  against each project's lockfiles, npm `ignore` semantics),
+  `ecosystems`, `packages` / `ignorePackages` (`--package` specs),
+  `minSeverity` (critical|high|medium|moderate|low, judged by the worst
+  advisory a patch fixes) and `maxNewPatches` (validated; the per-run cap
+  lands with `--max-new-patches`). List flags (`--ecosystems`,
+  `--package`, PATHs) only narrow further; `--min-severity` beats the
+  file's floor and `--no-socket-yml` ignores the file. A package
+  that already carries a patch is never removed, upgraded or replaced by
+  the policy: it is held and reported under `policy.retained[]`. New flags
+  `--min-severity` / `SOCKET_MIN_SEVERITY` and `--no-socket-yml` /
+  `SOCKET_NO_SOCKET_YML`; every successful `scan --json` result gains a
+  top-level `policy` block (`source`, `sha256`, `minSeverity`, `filtered[]`,
+  `retained[]`) and the human output a `Policy (socket.yml): …` line that
+  names every skipped project and every critical/high patch the severity
+  floor held back. In memory, selection is two-phase:
+  `selectHostedScanPaths` takes the root policy files' text
+  (`policyFiles`) and `noSocketYml`, applies the full path policy and
+  returns `policyPaths`, `policySha256` and `policyError`; the session
+  takes `noSocketYml` / `minSeverity` / `policyPaths` / `policySha256` and
+  its result carries `policy` or `policyError`.
+  `get` ignores the policy and warns `policy_bypassed`.
+
 - **`scan --package <name|purl>`** (repeatable or comma-separated, env
   `SOCKET_SCAN_PACKAGES`) scopes a scan to the named packages: a name
   (`lodash`, `@scope/pkg`, `group:artifact`) or a purl with or without its

Cargo.toml

@@ -59,6 +59,8 @@ serial_test = "=3.4.0"
 napi = { version = "=3.13.0", features = ["napi8", "tokio_rt"] }
 napi-derive = "=3.6.9"
 napi-build = "=2.5.0"
+serde-saphyr = { version = "=1.3.0", default-features = false, features = ["deserialize"] }
+ignore = "=0.4.33"
 
 [profile.release]
 strip = true

README.md

@@ -413,6 +413,10 @@ socket-patch scan 'services/*'                                   # directory glo
 hosted and vendored mode each PATH is a project directory, scanned as if it were
 `--cwd` under an `== <dir> ==` header; the worst exit code wins.
 
+To make the choice stick for everyone who runs `scan` in the repo (CI and the Socket
+autopatch bot included), put it in `socket.yml` instead — see
+[Roll out gradually](#roll-out-gradually-with-socketyml).
+
 ### Patch one specific CVE or advisory
 
 ```bash
@@ -647,6 +651,8 @@ socket-patch scan [PATHS]... [options]
 | `--prune` | — | Agent-mode garbage collection after the scan: remove manifest entries for packages no longer present in the crawl (installed trees + lockfiles — a wiped `node_modules` alone doesn't prune lockfile-listed entries) and delete orphan blob/diff-archive files (plus any legacy package archives). [Vendored](#vendor) packages are exempt from the crawl-based prune, but a vendored entry whose dependency has left the lockfile is reverted. Ignored, with a `redirect_prune_ignored` warning, in hosted mode; without a mode the scan is report-only. |
 | `--sync` | — | Shorthand for `--mode agent --prune`: the one-flag agent-mode auto-update run. |
 | `--batch-size <n>` | `SOCKET_BATCH_SIZE` | Packages per API request (default: `500` on the authenticated API, `100` on the public proxy). A request whose body would exceed 256 KiB is split into smaller ones. |
+| `--min-severity <level>` | `SOCKET_MIN_SEVERITY` | Only patch packages whose patch fixes an advisory of at least `critical`, `high`, `medium` (or `moderate`) or `low`; `none` lifts the floor. Overrides `patches.minSeverity` in socket.yml. Patches of unknown severity are skipped whenever a floor is set. |
+| `--no-socket-yml` | `SOCKET_NO_SOCKET_YML` | Ignore the repo's socket.yml patch policy for this run (the built-in test/fixture directory ignores still apply). |
 | `--all-releases` | `SOCKET_ALL_RELEASES` | Store patches for every release/distribution variant, not just the installed one — PyPI wheel/sdist, RubyGems platform, Maven classifier. Makes the manifest portable across environments (e.g. cross-platform CI caches). |
 | `--vex <path>` | `SOCKET_VEX` | On a successful scan, also write an OpenVEX 0.2.0 document to this path. See [Inline VEX](#inline-vex-on-apply--scan--vendor). |
 | `--vex-product`, `--vex-no-verify`, `--vex-doc-id`, `--vex-compact` | `SOCKET_VEX_*` | Passthrough to the embedded VEX builder; mirror the standalone [`vex`](#vex) knobs. Inert unless `--vex` is set. |
@@ -692,6 +698,72 @@ socket-patch scan --vex socket.vex.json
 > artifact is the patch); a newer available patch still appears in `updates[]` — re-run
 > `scan --mode vendored` to take it.
 
+#### Roll out gradually with socket.yml
+
+A `patches` block in the repo-root `socket.yml` (the file the Socket scanner already
+reads; keep `version: 2`) narrows what `scan` may patch, for every mode and for the
+in-memory engine behind the Socket autopatch bot. It can only narrow: nothing in it can
+name an endpoint or token, pick a mode, or turn off a safety check.
+
+```yaml
+# Critical first: widen by editing one line
+version: 2
+patches:
+  minSeverity: critical   # later: high, then low, then remove the key
+                          # (low still skips patches whose severity is unknown)
+```
+
+```yaml
+# One directory first (monorepo)
+version: 2
+patches:
+  includePaths:
+    - "/services/payments/"
+    # add "/services/checkout/" next sprint
+```
+
+```yaml
+# One ecosystem, hold one package
+version: 2
+patches:
+  ecosystems: [npm]
+  ignorePackages: ["pkg:npm/left-pad"]
+```
+
+```yaml
+# Pause: report only; existing patches stay in place
+version: 2
+patches:
+  enabled: false
+```
+
+- Paths are gitignore patterns (the same rules as `projectIgnorePaths`, which scan now
+  honors too), matched against each project's lockfiles: `"/services/payments/"`,
+  `"**/yarn.lock"`, `"examples/**"`. `test/`, `tests/`, `fixtures/`, `__fixtures__/`
+  and `testdata/` directories are skipped by default when scan discovers projects
+  (a directory glob such as `scan 'services/*'`); re-include one with a negation
+  (`ignorePaths: ["!/e2e/tests/"]`). A directory you name yourself is always scanned.
+  (The autopatch bot's tree listing skips those directories before it reads
+  socket.yml, so there a negation cannot bring one back.)
+- `packages` / `ignorePackages` take `--package` specs; prefer purls (`pkg:npm/core`),
+  because a bare name also matches other ecosystems and scoped packages (`core`
+  matches `@babel/core`).
+- Narrowing never removes a patch: a package that already carries one and is now
+  filtered out is left exactly as it is (reported under `policy.retained[]`). Use
+  `rollback` or `remove` to take a patch out.
+- A broken file fails the scan (exit 1, `errorCode: socket_yml_invalid`) before anything
+  is written, with the key and the fix in the message — a typo never widens the
+  rollout. `--no-socket-yml` ignores the file for one run.
+- `scan --json` reports what the policy did in a top-level `policy` block
+  (`jq '.policy.counts'`); the human output adds a `Policy (socket.yml): …` line that
+  names every skipped project and every critical/high patch the severity floor held
+  back (`--verbose` lists everything). `get` ignores the policy (explicit
+  intent) and warns `policy_bypassed`.
+
+Every key: `enabled`, `includePaths`, `ignorePaths`, `ecosystems`, `packages`,
+`ignorePackages`, `minSeverity`, `maxNewPatches` — see CLI_CONTRACT.md "socket.yml patch
+policy" for the full grammar, precedence and validation rules.
+
 ### `vex`
 
 Generate an [OpenVEX](https://github.com/openvex) 0.2.0 attestation describing the