dep-up-surgeon 2.2.2 → 2.2.4

package/README.md

@@ -79,8 +79,9 @@ dep-up-surgeon [options]
 | `--security-only` | Run `npm audit` (or `pnpm`/`yarn` equivalent) first, then upgrade **only** the packages with open advisories. Every successful bump carries the advisory severity + ID into its commit subject (`[security:high]`) and into the summary's **Security fixes** table. Pairs well with `--git-commit-mode per-success` to produce one PR per CVE. See **Security-first mode** below. |
 | `--min-severity <level>` | Minimum advisory severity to consider under `--security-only`: `low` (default), `moderate`, `high`, or `critical`. Lower-severity advisories are filtered out before the upgrade plan is built. |
 | `--blast-radius` / `--no-blast-radius` | Scan project source files to list which files actually `import`/`require` each upgraded package, and surface the list in `--json` + `--summary`. **Default ON** when `--summary` is active. See **Blast radius** below. |
-| `--resolve-peers` / `--no-resolve-peers` | When a linked-group bump (e.g. `react` + `react-dom` + `@types/react`) fails with a peer-dependency conflict, compute the intersection of peer ranges across the registry packument and retry with a satisfiable version tuple (members may land below `latest`). **Default ON**. See **Peer-range intersection resolver** below. |
+| `--resolve-peers` / `--no-resolve-peers` | When a linked-group bump (e.g. `react` + `react-dom` + `@types/react`) **or a single-package bump** fails with a peer-dependency conflict, compute the intersection of peer ranges across the registry packument and retry with a satisfiable version tuple (members may land below `latest`). Linked graphs with 10+ members automatically use a SAT-style AC-3 solver; single-package failures synthesize an **ad-hoc group** from direct-dep blockers named in the install output. **Default ON**. See **Peer-range intersection resolver** below. |
 | `--apply-overrides` | After the main upgrade loop, fix **transitive** CVEs that no direct bump could reach by writing a package-manager override (`overrides` for npm, `pnpm.overrides` for pnpm, `resolutions` for yarn) pinning each vulnerable transitive to its audit-recommended safe version. Runs install + validator after each pin and rolls back automatically when the validator fails. Requires `--security-only`. See **Transitive overrides** below. |
+| `--override <spec...>` | Apply one or more **manual** override pins independent of the audit. Repeatable and also accepts comma-separated values. Syntax: `<chain>@<range>`, where `<chain>` is a bare name (`lodash`), a pnpm-style chain (`some-dep>foo`, any depth), or a yarn-style chain (`parent/child`). Scoped names (`@scope/pkg`) are preserved as single chain segments. Written to the manager-native nested form (npm object, pnpm `>`-keys, yarn `/`-keys) and run through the same install + validator + rollback loop as `--apply-overrides`. Works standalone — `--security-only` is not required. See **Transitive overrides** below. |
 | `--override-force` | Used with `--apply-overrides`. Overwrite an **existing** override entry whose value conflicts with the audit-recommended version. By default we refuse to clobber user-managed pins and record `conflict` in the report. |
 | `--fix-lockfile` | After the main upgrade loop, run the package manager's native dedupe command (`npm dedupe` / `pnpm dedupe` / `yarn dedupe`) to collapse redundant transitive copies **without touching `package.json`**, and flag transitives more than a minor or a full major behind registry `latest`. Lockfile is backed up before dedupe and restored if dedupe OR the post-dedupe validator fails. Yarn classic (v1) has no dedupe subcommand — recorded as `skipped: "unsupported"`. See **Lockfile fix** below. |
 | `--open-pr` | After `--git-commit --git-branch` pushes the branch, open a GitHub PR with the `--summary` markdown as the body (falls back to a deterministic minimal body). Uses the `gh` CLI (must be installed + authenticated); never fatal — a missing binary, auth failure, or push rejection is recorded as `pullRequest.error` in the JSON report without aborting the run. See **Auto-opening a PR** below. |
@@ -235,6 +236,8 @@ npx dep-up-surgeon --workspaces --security-only --min-severity high \
   --git-branch "deps/security-$(date +%Y-%m-%d)"
 ```
 
+The whole path is covered by `test/unit/security-only.test.mjs` — a hermetic regression harness that drives `runAudit` with a canned `npm audit --json` blob, asserts `--min-severity` filters at every tier, and exercises the full `runUpgradeFlow` → install → validator → **rollback** cycle without touching the registry (via the `UpgradeFlowOptions.installer` injection point).
+
 ### Policy engine (policy-as-code)
 
 Drop a `.dep-up-surgeon.policy.yaml` (or `.json`) in the repo root to encode upgrade rules that survive across runs and humans. Loaded automatically on startup; violations are reported per-package and the engine skips the offending bumps instead of failing.
@@ -296,16 +299,21 @@ Linked-group bumps (e.g. `react` + `react-dom` + `@types/react`, or the Jest / T
 2. If the install fails with a **peer** conflict, the resolver fetches each linked package's full registry packument (cached — one call per package per run) and reads every published version's `peerDependencies` block.
 3. Each member gets a candidate domain: every version between `currentRange`'s `minVersion` and the originally-requested target, sorted newest-first, minus deprecated / pre-release versions.
 4. A **newest-first backtracking search** enumerates version tuples (variable = one package, domain = its candidate versions). For each partial assignment, every peer constraint that has become knowable is checked; peers on packages inside the linked group are checked against the chosen version, peers on packages OUTSIDE the group are checked against that package's range in the current `package.json` (via `semver.minVersion`).
-5. The **first** complete tuple to satisfy every constraint is also the least-downgrade one. The engine rewrites the batch's target versions and retries the install + validator. On success, every affected row is tagged with `resolvedPeer = { originalTarget, reason, tuplesExplored }`.
-6. If the resolver can't find a satisfiable tuple, or the retried install still fails, the batch falls back to the pre-resolver behavior (rollback + `kind: 'peer'` failure row).
+5. For **large linked graphs (≥ 10 members)** — where the 400-tuple backtracking budget can be burned before the solver escapes the first variable's domain — the resolver automatically switches to a **SAT-style path** (arc-consistency + least-constraining-value DFS). It pre-prunes every member-version that can't be satisfied against external peers, runs up to 128 AC-3 rounds across every ordered member pair until the pruned domains reach a fixed point, then does an **MRV-ordered** (smallest domain first) newest-first DFS on whatever survived. For monorepo link groups up to ~50 members × ~30 recent versions this finishes in milliseconds where plain DFS would return `undefined`. When the SAT path fails the dispatcher falls back to the plain backtracker automatically.
+6. The **first** complete tuple to satisfy every constraint is also the least-downgrade one. The engine rewrites the batch's target versions and retries the install + validator. On success, every affected row is tagged with `resolvedPeer = { originalTarget, reason, tuplesExplored }` — `reason` carries a `[backtracking]` or `[sat]` method tag so reviewers can tell which solver path produced the tuple.
+7. If the resolver can't find a satisfiable tuple, or the retried install still fails, the batch falls back to the pre-resolver behavior (rollback + `kind: 'peer'` failure row).
+
+**Ad-hoc resolver for non-linked bumps.** Single-package upgrades that fail with a peer conflict used to be rolled back unconditionally — the resolver was linked-groups-only. Now we synthesize an **ad-hoc group** from the parsed install output: the primary + every blocker named in the peer-conflict lines that's **already a direct dep** of the workspace (peers on unknown transitives stay out of scope). The same resolver (and the same SAT fallback) runs on that synthesized group. On success the engine writes a small batch: the primary at whatever version the resolver picked, plus any blocker the resolver wants moved within its **current pinned range** (the ad-hoc path is allowed to downgrade the primary, never to silently bump a blocker past its pin).
 
 Guard rails that keep it safe:
 
-- **Bounded search** — capped at 400 tuples explored per batch. Past that the resolver gives up silently instead of hanging the run on pathological inputs.
+- **Bounded search** — capped at 400 tuples explored per batch (small graphs) or `400 × members` tuples for the SAT path's DFS phase. Past that the resolver gives up silently instead of hanging the run on pathological inputs.
 - **Optional peers** (`peerDependenciesMeta[name].optional === true`) are ignored. An unsatisfied optional peer isn't a hard conflict.
 - **Deprecated versions** never appear in the domain. We'd rather fail to find a solution than auto-suggest a known-bad version.
+- **Ad-hoc group size cap** — default 6 members (primary + up to 5 direct-dep blockers). Prevents registry fetch storms on pathological peer graphs.
+- **Ad-hoc never adds dependencies** — a peer on a transitive that isn't already a direct dep is ignored rather than introduced.
 - **`--force` bypasses the resolver** — the user has explicitly opted into barreling through peer conflicts.
-- **`--no-resolve-peers`** keeps the old behavior when you WANT peer failures to surface so a human resolves them instead of the tool silently nudging versions off latest.
+- **`--no-resolve-peers`** keeps the old behavior when you WANT peer failures to surface so a human resolves them instead of the tool silently nudging versions off latest. Applies to both the linked-group and ad-hoc paths.
 
 Where it shows up:
 
@@ -314,7 +322,7 @@ Where it shows up:
 - **Commit subjects**: `[peer-resolved]` tag sits between `[breaking]` and `[security:<sev>]` (stable order). The body gets a `Peer-range resolutions (kept linked group satisfiable):` footer listing each pinned member.
 - **`--json`**: `upgraded[].resolvedPeer = { originalTarget, reason, tuplesExplored }` plus `upgraded[].requestedLatest` still reflects the pre-resolver target so downstream tools can diff them.
 
-### Transitive overrides (`--apply-overrides`)
+### Transitive overrides (`--apply-overrides` / `--override`)
 
 `--security-only` by itself can only fix vulnerabilities reachable from a direct dependency. For CVEs that live in transitives (very common — `lodash@4.17.20` buried six levels deep under a toolchain package), pair `--security-only` with `--apply-overrides` and the tool will write a package-manager override to pin the vulnerable transitive to its safe version.
 
@@ -323,19 +331,117 @@ Where it shows up:
 - **Rollback on failure**: after each override, the tool runs a full install and then the validator. If either fails, the override is removed, install re-runs to restore the starting state, and the next advisory is still attempted. A failed override never strands the workspace — `report.overrides.attempts[].rolledBack === true` appears in the JSON and the summary.
 - **Conflict protection**: when the user already has a manual override with a value that **conflicts** with the audit recommendation, we refuse to clobber by default (`reason: "conflicts with target ..."`). Pass `--override-force` to overwrite explicitly.
 - **Where it shows up**:
-  - **`--summary`**: dedicated `Overrides applied` table with `Package / Pinned to / Severity / Advisory`.
-  - **`--json`**: `overrides.field` + `overrides.attempts[]` with the full decision trail (`ok`, `skipped`, `reason`, `previous`, `applied`, `installLog`, `rolledBack`).
+  - **`--summary`**: dedicated `Overrides applied` table with `Package / Pinned to / Source / Severity / Advisory`. Parent-scoped pins render as `a › b › c` so the chain is visible at a glance.
+  - **`--json`**: `overrides.field` + `overrides.attempts[]` with the full decision trail (`ok`, `skipped`, `reason`, `previous`, `applied`, `installLog`, `rolledBack`, `chain`, `source`). Parent-scoped pins carry `chain: ["parent", "child"]`; `source` distinguishes `"advisory"` from `"manual"`.
+
+#### Parent-scoped pins (`--override`)
+
+`--apply-overrides` only writes the **flat** `name → version` form — every occurrence of the package gets pinned. When you need to pin a transitive **only when it appears under a specific parent** (e.g. you want `foo@1.2.3` under `some-dep` while the rest of the tree uses `foo@2.x`), use `--override` to write a **parent-scoped** selector. Works standalone — no `--security-only` required.
+
+Syntax: `<chain>@<range>`. The chain supports three forms, all normalized internally:
+
+- **Flat**: `--override lodash@4.17.21` → same shape as a classic flat override.
+- **pnpm-style**: `--override "some-dep>foo@1.2.3"` — pin `foo` only when nested under `some-dep`. Chains of any depth (`a>b>c>d@1.0.0`) are supported.
+- **yarn-style**: `--override "parent/child@1.2.3"` — `/` separator; `@scope/pkg` stays intact as a single chain segment.
+
+Each selector is written to the **manager's native nested encoding**:
+
+| Manager | Shape written |
+| --- | --- |
+| npm | `{ "overrides": { "some-dep": { "foo": "1.2.3" } } }` — nested object; an existing flat pin for the parent is preserved via npm's `"."` self-selector. |
+| pnpm | `{ "pnpm": { "overrides": { "some-dep>foo": "1.2.3" } } }` — pnpm's `>`-chain keys, deep chains supported. |
+| yarn | `{ "resolutions": { "some-dep/foo": "1.2.3" } }` — `/`-chain keys. |
+
+Every pin runs through the same install + validator + rollback loop as advisory-driven pins. A failed manual pin is rolled back (only that specific slot) and the rest of the run continues; a flat pin and a parent-scoped pin with the same leaf name coexist as separate entries.
 
 ```bash
-# Weekly security sweep: direct bumps first, then transitive overrides, then a draft PR.
+# Pin `lodash@4.17.21` ONLY when it's a transitive of `some-dep`, and pin `axios@1.6.0`
+# globally. Both live in the same run; one failing never touches the other.
+npx dep-up-surgeon \
+  --override "some-dep>lodash@4.17.21" \
+  --override "axios@1.6.0" \
+  --validate "npm test"
+```
+
+```bash
+# Weekly security sweep: direct bumps first, then transitive overrides (audit-driven +
+# one manual pin), then a draft PR.
 npx dep-up-surgeon --workspaces \
   --security-only --min-severity high \
   --apply-overrides \
+  --override "@babel/core>@babel/traverse@7.23.2" \
   --git-commit --git-commit-mode per-success --git-branch "deps/security-$(date +%Y-%m-%d)" \
   --summary md \
   --open-pr --open-pr-draft
 ```
 
+#### Override policy file (`.dep-up-surgeonrc` `overrides`)
+
+Re-typing `--override "parent>child@1.2.3"` on every CI run gets old fast. Commit the pins to `.dep-up-surgeonrc` instead and they'll apply on every run the same way `ignore` does — merging with any CLI `--override` flags on the same invocation (**CLI wins on chain conflict**). The committed form supports a `reason` string that flows straight into the report + summary so reviewers can see **why** each transitive is pinned (CVE ID, vendor guidance, upstream PR link) without grepping commit history.
+
+Two input shapes are accepted:
+
+```jsonc
+{
+  "overrides": [
+    // Structured: explicit chain + range. `chain: "lodash"` is shorthand for the flat case.
+    { "chain": ["some-dep", "foo"], "range": "1.2.3", "reason": "CVE-2025-1234" },
+
+    // Selector form: same syntax as the `--override` CLI flag.
+    { "selector": "@babel/core>@babel/traverse@7.23.2", "reason": "upstream PR #16012 pending" },
+    { "selector": "lodash@4.17.21" }
+  ]
+}
+```
+
+Behavior:
+
+- **Merge + dedupe**: entries are merged with CLI `--override` selectors by exact chain. A CLI pin for the same chain **replaces** the rc entry (including the `reason`), so one-off ad-hoc overrides always win over committed policy.
+- **Malformed CLI selectors are warnings**, not fatal: a typo in one `--override` flag won't prevent committed rc pins from applying. rc entries with a bad shape produce per-entry warnings in `.dep-up-surgeonrc.warnings` and the run continues.
+- **Same lifecycle as `--override`**: every pin goes through the install + validator + rollback loop. Failures are per-pin — one bad pin never strands the rest.
+- **`reason` surfaces in the report**: the `Overrides applied` table in `--summary` adds a `Reason` column whenever at least one attempt carries one; `--json` ships `overrides.attempts[].policyReason` verbatim for bots.
+
+```bash
+# Run the committed overrides policy. No CLI flags needed; `overrides: [...]` in
+# `.dep-up-surgeonrc` is enough to trigger the flow.
+npx dep-up-surgeon --summary md
+
+# Add a one-off pin on top of the committed set for this run only:
+npx dep-up-surgeon --override "lodash@4.17.21" --summary md
+```
+
+### Disaster recovery (`dep-up-surgeon undo`)
+
+Every run writes `.dep-up-surgeon.last-run.json` — a structured record of what the tool did (previous ranges, `to` values, every override attempt with `applied`/`previous`, workspace targets). `dep-up-surgeon undo` replays that record **in reverse**:
+
+1. For every successful upgrade row, write the recorded `from` back to `package.json` (in whatever section currently holds the dep, across the root and every workspace target).
+2. For every successful override attempt, drop the pin we added — or, when the attempt recorded a `previous` value (the run replaced an existing pin), restore that previous value.
+3. Run `<manager> install` once per edited target so the lockfile re-converges to the reverted `package.json`.
+4. Run the validator so you see green/red before you commit the revert.
+
+Drift protection:
+
+- If the current `package.json` value for a dep **doesn't match** the `to` the run landed on (another run, or a human edit, moved it), the row is **skipped** with `reason: 'drifted'`. Undo never rewrites state we don't recognize.
+- When the recorded run was `--dry-run`, undo is a **no-op**.
+- Missing / unparseable run report → the command exits with status 2 and a clear error message.
+
+```bash
+# Replay the newest recorded run in this directory.
+npx dep-up-surgeon undo
+
+# Compute the reverse plan WITHOUT touching the disk. Use for review/CI dry-runs.
+npx dep-up-surgeon undo --dry-run
+
+# Replay a specific run file (e.g. from a CI artifact).
+npx dep-up-surgeon undo --file ./ci-logs/2026-04-18-upgrade.last-run.json
+
+# Skip the validator — handy when the project has no test script but you still want the
+# dep ranges rolled back.
+npx dep-up-surgeon undo --no-validate
+```
+
+Exit codes: `0` = reverse pass succeeded (or was a no-op); `1` = install or validator failed during the reverse pass (the JSON report still explains which rows moved); `2` = the run report was missing / invalid. Pair with `--json` for CI pipelines — the full `UndoResult` is emitted on stdout.
+
 ### Lockfile fix (`--fix-lockfile`)
 
 `--fix-lockfile` improves the **lockfile's** dependency graph without touching `package.json`. It's the counterpart to `--apply-overrides`: where overrides fix vulnerable transitives, `--fix-lockfile` collapses redundant ones and surfaces the stale-but-not-vulnerable tail that a direct upgrade loop can never reach.
@@ -508,7 +614,11 @@ Create `.dep-up-surgeonrc` in the project root:
       "packages": ["package-a", "package-b"]
     }
   ],
-  "validate": "tsc -p tsconfig.json --noEmit"
+  "validate": "tsc -p tsconfig.json --noEmit",
+  "overrides": [
+    { "chain": ["some-dep", "foo"], "range": "1.2.3", "reason": "CVE-2025-1234" },
+    { "selector": "lodash@4.17.21", "reason": "awaiting upstream PR #42" }
+  ]
 }
 ```
 
@@ -518,6 +628,8 @@ Ignored packages are never upgraded. The CLI `--ignore` list is merged with this
 
 **`validate`** overrides the validator command. Accepts either a shell string (`"tsc --noEmit"`) or an object: `{ "command": "pnpm -r build" }` or `{ "skip": true }`. CLI flags (`--validate`, `--no-validate`) always win over this file.
 
+**`overrides`** defines persistent parent-scoped / flat override pins applied on every run. Merges with CLI `--override` flags (CLI wins on exact-chain conflict). Each entry's `reason` flows into `report.overrides.attempts[].policyReason` and the summary's `Reason` column. See [Override policy file](#override-policy-file-dep-up-surgeonrc-overrides) for the full schema.
+
 ## JSON report (`--json`)
 
 Stdout is a single JSON object including:
@@ -605,8 +717,6 @@ The compiled entry is `dist/cli.js` (see `"bin"` in `package.json`).
 ## Future work (tracked in code)
 
 - GitLab / Bitbucket auto-PR providers (today `--open-pr` is GitHub-only via `gh`)
-- Nested / parent-scoped override rules beyond the flat `name → version` form (`overrides: { "foo": { ">=2 <3": "3.0.0" } }` in npm, deep pnpm selectors)
-- Resolver sharpening: SAT-backed peer-range intersection for very large linked graphs (10+ members) where the current 400-tuple backtracking budget gives up; peer-range intersection across **non-linked** packages too (today the resolver only intervenes on linked-group failures)
 - Renovate-style scheduling helpers (cron / day-of-week filters, grouping rules)
 - True parallel installs in monorepos that don't share a root lockfile (e.g. nohoist setups), going beyond today's parallel scan + serial install model
 - AI-assisted failure explanation: feed `install.lastLines` + `validation.lastLines` to an LLM and attach a one-sentence "why this broke" note to failed records

package/dist/cli/overrideFlow.d.ts

@@ -1,5 +1,6 @@
 import type { SecurityAdvisory } from '../core/audit.js';
 import type { PackageManager } from '../core/workspaces.js';
+import { runInstall } from '../utils/npm.js';
 import { type OverrideField } from '../utils/overrides.js';
 export interface OverrideAttemptRecord {
     name: string;
@@ -11,6 +12,25 @@ export interface OverrideAttemptRecord {
     applied?: string;
     /** The previous pin, if any. */
     previous?: string;
+    /**
+     * Full parent chain for parent-scoped pins, outermost → leaf. Omitted for flat pins
+     * (equivalent to `chain: [name]`). Included in the report so consumers know which exact
+     * slot in the overrides block was touched.
+     */
+    chain?: string[];
+    /**
+     * How this attempt was triggered. `advisory` = fed in by `--security-only` audit; `manual`
+     * = user-supplied via `--override` CLI flag or `.dep-up-surgeonrc` `overrides` policy.
+     * Consumers can render the two lists separately (e.g. manual overrides don't map to a CVE).
+     */
+    source: 'advisory' | 'manual';
+    /**
+     * Human-readable reason the manual pin exists (e.g. `"CVE-2025-1234"`, `"awaiting upstream
+     * PR #123"`). Populated only for pins sourced from the rc policy; CLI-only pins have no
+     * reason attached. Rendered verbatim in the JSON report and the markdown summary so
+     * reviewers see the "why" next to the "what" without grepping commit messages.
+     */
+    policyReason?: string;
     /** Field we touched (`overrides` / `pnpm.overrides` / `resolutions`). */
     field: OverrideField;
     /** True when the write, install, AND validator all succeeded. */
@@ -24,6 +44,25 @@ export interface OverrideAttemptRecord {
     /** True when a rollback was performed. */
     rolledBack?: boolean;
 }
+/**
+ * User-supplied override pin (from `--override` CLI flag or similar). Unlike advisory-driven
+ * pins, these carry an arbitrary parent chain and no CVE metadata. They run through the same
+ * write + install + validator + rollback cycle so a manual pin can't wreck the workspace.
+ */
+export interface ManualOverrideSpec {
+    /** Parent chain + leaf, outermost → leaf (`[name]` for flat pins). */
+    chain: string[];
+    /** Version / range to pin. */
+    range: string;
+    /** Original user-supplied selector string, for error messages and the report. */
+    source?: string;
+    /**
+     * Optional human-readable reason for the pin. When provided, it's threaded into the
+     * attempt record's `policyReason` so the JSON report + summary can render it alongside
+     * the pinned package. Used by rc-sourced overrides to surface CVE IDs / vendor guidance.
+     */
+    reason?: string;
+}
 export interface OverrideFlowOptions {
     /** Workspace root. Every override write and `runInstall` happens here. */
     cwd: string;
@@ -49,6 +88,17 @@ export interface OverrideFlowOptions {
     dryRun?: boolean;
     /** True when the CLI is in `--json` mode: suppress human-readable progress log lines. */
     json?: boolean;
+    /**
+     * User-supplied parent-scoped or flat pins (via `--override` CLI flag). These run AFTER
+     * the advisory-driven pins in the same loop so they share the install + validator +
+     * rollback machinery. A failure here never touches advisory results.
+     */
+    manualOverrides?: ManualOverrideSpec[];
+    /**
+     * Optional install runner override. Kept as an injection point so tests can exercise the
+     * write + rollback cycle without actually shelling out.
+     */
+    installer?: typeof runInstall;
 }
 export interface OverrideFlowResult {
     /** Every advisory we considered, including skips. */

package/dist/cli/overrideFlow.d.ts.map

@@ -1 +1 @@
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package/dist/cli/overrideFlow.js

@@ -41,10 +41,11 @@ export async function runOverrideFlow(opts) {
     // the main upgrade loop. These are the pure-transitive CVEs that overrides exist to fix.
     const targets = opts.advisories.filter((a) => !opts.directDepNames.has(a.name) &&
         !opts.upgradedNames.has(a.name));
-    if (targets.length === 0) {
+    const hasManual = (opts.manualOverrides?.length ?? 0) > 0;
+    if (targets.length === 0 && !hasManual) {
         return { attempts };
     }
-    if (!opts.json) {
+    if (targets.length > 0 && !opts.json) {
         log.info(`--apply-overrides: ${targets.length} transitive advisor${targets.length === 1 ? 'y' : 'ies'} to pin (${targets.map((t) => t.name).slice(0, 5).join(', ')}${targets.length > 5 ? ', ...' : ''})`);
     }
     for (const adv of targets) {
@@ -55,6 +56,7 @@ export async function runOverrideFlow(opts) {
             field,
             ok: false,
             skipped: false,
+            source: 'advisory',
         };
         if (adv.url)
             rec.url = adv.url;
@@ -67,90 +69,131 @@ export async function runOverrideFlow(opts) {
             attempts.push(rec);
             continue;
         }
-        if (opts.dryRun) {
-            rec.skipped = true;
-            rec.reason = 'dry-run';
-            rec.applied = target;
-            attempts.push(rec);
-            continue;
-        }
-        // 1. Write the pin (or skip when already safe).
-        const applied = await applyOverrideToFile({
-            packageJsonPath: pkgJson,
-            manager: opts.manager,
-            entry: { name: adv.name, range: target },
-            ...(opts.overwriteConflicts ? { overwriteConflicts: true } : {}),
-        });
-        if (!applied.ok) {
-            rec.skipped = true;
-            rec.reason = applied.reason;
-            if (applied.previous)
-                rec.previous = applied.previous;
-            attempts.push(rec);
-            continue;
+        await processPin(rec, { name: adv.name, range: target }, opts, pkgJson, `--apply-overrides`);
+        attempts.push(rec);
+    }
+    // Manual --override pins: processed AFTER advisories so any audit-driven pin that clears a
+    // path is visible first. Manual pins share the same install + validator + rollback loop.
+    if (opts.manualOverrides && opts.manualOverrides.length > 0) {
+        if (!opts.json) {
+            log.info(`--override: ${opts.manualOverrides.length} manual pin${opts.manualOverrides.length === 1 ? '' : 's'} to apply`);
         }
-        if (!applied.written) {
-            // No-op (already satisfies). Record as skip but mark ok: true so the summary doesn't
-            // mistake it for a failure.
-            rec.skipped = true;
-            rec.ok = true;
-            rec.reason = applied.reason ?? 'already satisfies target';
-            if (applied.applied)
-                rec.applied = applied.applied;
-            if (applied.previous)
-                rec.previous = applied.previous;
+        for (const spec of opts.manualOverrides) {
+            if (spec.chain.length === 0)
+                continue;
+            const name = spec.chain[spec.chain.length - 1];
+            const parentChain = spec.chain.slice(0, -1);
+            const rec = {
+                name,
+                severity: 'low',
+                ids: [],
+                field,
+                ok: false,
+                skipped: false,
+                source: 'manual',
+            };
+            if (spec.chain.length > 1)
+                rec.chain = [...spec.chain];
+            if (spec.source)
+                rec.title = spec.source;
+            if (spec.reason)
+                rec.policyReason = spec.reason;
+            const entry = { name, range: spec.range };
+            if (parentChain.length > 0)
+                entry.parentChain = parentChain;
+            await processPin(rec, entry, opts, pkgJson, `--override`);
             attempts.push(rec);
-            continue;
         }
-        rec.applied = applied.applied ?? target;
+    }
+    return { attempts };
+}
+/**
+ * Shared write + install + validate + rollback cycle used for BOTH advisory pins and
+ * manual pins. Mutates `rec` in place: callers push it into `attempts` regardless of
+ * outcome. Returns nothing — every outcome is captured on `rec`.
+ */
+async function processPin(rec, entry, opts, pkgJson, logTag) {
+    const label = entry.parentChain && entry.parentChain.length > 0
+        ? `${[...entry.parentChain, entry.name].join('>')}`
+        : entry.name;
+    if (opts.dryRun) {
+        rec.skipped = true;
+        rec.reason = 'dry-run';
+        rec.applied = entry.range;
+        return;
+    }
+    const applied = await applyOverrideToFile({
+        packageJsonPath: pkgJson,
+        manager: opts.manager,
+        entry,
+        ...(opts.overwriteConflicts ? { overwriteConflicts: true } : {}),
+    });
+    if (!applied.ok) {
+        rec.skipped = true;
+        rec.reason = applied.reason;
         if (applied.previous)
             rec.previous = applied.previous;
-        // 2. Install with the new pin.
-        if (!opts.json) {
-            log.info(`--apply-overrides: pinning ${adv.name} → ${target} and running ${opts.manager} install`);
-        }
-        const install = await runInstall(opts.cwd, opts.manager, {});
-        if (!install.ok) {
-            rec.installLog = tailOutput(install);
-            const rb = await rollback(pkgJson, opts, adv.name);
-            rec.rolledBack = rb.rolledBack;
-            rec.reason = `install failed after override (exit ${install.exitCode})`;
-            attempts.push(rec);
-            continue;
-        }
-        // 3. Validator (when provided).
-        if (opts.runValidator) {
-            const v = await opts.runValidator();
-            if (!v.ok) {
-                rec.installLog = v.message;
-                const rb = await rollback(pkgJson, opts, adv.name);
-                rec.rolledBack = rb.rolledBack;
-                rec.reason = `validator failed after override: ${v.message ?? 'non-zero exit'}`;
-                attempts.push(rec);
-                continue;
-            }
-        }
+        return;
+    }
+    if (!applied.written) {
+        rec.skipped = true;
         rec.ok = true;
-        attempts.push(rec);
-        if (!opts.json) {
-            log.success(`--apply-overrides: pinned ${adv.name}@${target} (severity: ${adv.severity})`);
+        rec.reason = applied.reason ?? 'already satisfies target';
+        if (applied.applied)
+            rec.applied = applied.applied;
+        if (applied.previous)
+            rec.previous = applied.previous;
+        return;
+    }
+    rec.applied = applied.applied ?? entry.range;
+    if (applied.previous)
+        rec.previous = applied.previous;
+    if (!opts.json) {
+        log.info(`${logTag}: pinning ${label} → ${entry.range} and running ${opts.manager} install`);
+    }
+    const installer = opts.installer ?? runInstall;
+    const install = await installer(opts.cwd, opts.manager, {});
+    if (!install.ok) {
+        rec.installLog = tailOutput(install);
+        const rb = await rollback(pkgJson, opts, entry);
+        rec.rolledBack = rb.rolledBack;
+        rec.reason = `install failed after override (exit ${install.exitCode})`;
+        return;
+    }
+    if (opts.runValidator) {
+        const v = await opts.runValidator();
+        if (!v.ok) {
+            if (v.message)
+                rec.installLog = v.message;
+            const rb = await rollback(pkgJson, opts, entry);
+            rec.rolledBack = rb.rolledBack;
+            rec.reason = `validator failed after override: ${v.message ?? 'non-zero exit'}`;
+            return;
         }
     }
-    return { attempts };
+    rec.ok = true;
+    if (!opts.json) {
+        log.success(`${logTag}: pinned ${label}@${entry.range}`);
+    }
 }
 /**
  * Remove the override we just added and re-run install so the workspace ends up in the same
- * state the user had at the start of the attempt. Install failures during rollback are logged
+ * state the user had at the start of the attempt. The entry's parent chain (if any) is
+ * threaded through to `removeOverrideFromFile` so we delete the EXACT slot we wrote and
+ * never touch an adjacent flat pin or sibling. Install failures during rollback are logged
  * but don't crash the flow — the next override attempt will run whatever state we're in.
  */
-async function rollback(pkgJson, opts, name) {
-    const removed = await removeOverrideFromFile(pkgJson, opts.manager, name);
+async function rollback(pkgJson, opts, entry) {
+    const chain = [...(entry.parentChain ?? []), entry.name];
+    const label = chain.join('>');
+    const removed = await removeOverrideFromFile(pkgJson, opts.manager, { chain });
     if (!removed.ok || !removed.removed) {
         return { rolledBack: false, reinstallOk: false };
     }
-    const reinstall = await runInstall(opts.cwd, opts.manager, {});
+    const installer = opts.installer ?? runInstall;
+    const reinstall = await installer(opts.cwd, opts.manager, {});
     if (!reinstall.ok && !opts.json) {
-        log.warn(`rollback: re-install after removing override for ${name} exited ${reinstall.exitCode}; workspace may need manual cleanup.`);
+        log.warn(`rollback: re-install after removing override for ${label} exited ${reinstall.exitCode}; workspace may need manual cleanup.`);
     }
     return { rolledBack: true, reinstallOk: reinstall.ok };
 }

package/dist/cli/overrideFlow.js.map

@@ -1 +1 @@
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package/dist/cli/summary.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"summary.d.ts","sourceRoot":"","sources":["../../src/cli/summary.ts"],"names":[],"mappings":"AAGA,OAAO,KAAK,EAAE,gBAAgB,EAAE,MAAM,aAAa,CAAC;AAgDpD,MAAM,MAAM,aAAa,GAAG,IAAI,GAAG,MAAM,CAAC;AAE1C,MAAM,WAAW,mBAAmB;IAClC,MAAM,EAAE,aAAa,CAAC;IACtB,uFAAuF;IACvF,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,iEAAiE;IACjE,GAAG,EAAE,MAAM,CAAC;IACZ,qEAAqE;IACrE,WAAW,EAAE,MAAM,CAAC;IACpB,kEAAkE;IAClE,GAAG,CAAC,EAAE,MAAM,CAAC,UAAU,CAAC;CACzB;AAID;;;;;;GAMG;AACH,wBAAgB,yBAAyB,CAAC,IAAI,EAAE,mBAAmB,GAAG;IAAE,IAAI,EAAE,MAAM,CAAC;IAAC,MAAM,EAAE,OAAO,CAAA;CAAE,CActG;AAED,wBAAsB,YAAY,CAChC,UAAU,EAAE,gBAAgB,EAC5B,IAAI,EAAE,mBAAmB,GACxB,OAAO,CAAC,MAAM,GAAG,SAAS,CAAC,CAgB7B;AAoBD,wBAAgB,qBAAqB,CAAC,UAAU,EAAE,gBAAgB,EAAE,WAAW,EAAE,MAAM,GAAG,MAAM,CA8S/F;AAED,wBAAgB,iBAAiB,CAAC,UAAU,EAAE,gBAAgB,EAAE,WAAW,EAAE,MAAM,GAAG,MAAM,CAwN3F"}
+{"version":3,"file":"summary.d.ts","sourceRoot":"","sources":["../../src/cli/summary.ts"],"names":[],"mappings":"AAGA,OAAO,KAAK,EAAE,gBAAgB,EAAE,MAAM,aAAa,CAAC;AAgDpD,MAAM,MAAM,aAAa,GAAG,IAAI,GAAG,MAAM,CAAC;AAE1C,MAAM,WAAW,mBAAmB;IAClC,MAAM,EAAE,aAAa,CAAC;IACtB,uFAAuF;IACvF,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,iEAAiE;IACjE,GAAG,EAAE,MAAM,CAAC;IACZ,qEAAqE;IACrE,WAAW,EAAE,MAAM,CAAC;IACpB,kEAAkE;IAClE,GAAG,CAAC,EAAE,MAAM,CAAC,UAAU,CAAC;CACzB;AAID;;;;;;GAMG;AACH,wBAAgB,yBAAyB,CAAC,IAAI,EAAE,mBAAmB,GAAG;IAAE,IAAI,EAAE,MAAM,CAAC;IAAC,MAAM,EAAE,OAAO,CAAA;CAAE,CActG;AAED,wBAAsB,YAAY,CAChC,UAAU,EAAE,gBAAgB,EAC5B,IAAI,EAAE,mBAAmB,GACxB,OAAO,CAAC,MAAM,GAAG,SAAS,CAAC,CAgB7B;AAoBD,wBAAgB,qBAAqB,CAAC,UAAU,EAAE,gBAAgB,EAAE,WAAW,EAAE,MAAM,GAAG,MAAM,CA4T/F;AAED,wBAAgB,iBAAiB,CAAC,UAAU,EAAE,gBAAgB,EAAE,WAAW,EAAE,MAAM,GAAG,MAAM,CAwN3F"}

package/dist/cli/summary.js

@@ -303,18 +303,31 @@ export function renderSummaryMarkdown(structured, toolVersion) {
         lines.push(`_wrote to \`${structured.overrides.field}\` — ${ok.length} pinned, ${noOp.length} already safe, ${failed.length} failed._`);
         lines.push('');
         if (ok.length > 0) {
-            lines.push(`| Package | Pinned to | Severity | Advisory |`);
-            lines.push(`| --- | --- | --- | --- |`);
+            // Show the `Reason` column only when at least one pin carries a policy reason — keeps
+            // the table narrow for the common advisory-only case.
+            const hasReason = ok.some((a) => typeof a.policyReason === 'string' && a.policyReason);
+            const header = hasReason
+                ? `| Package | Pinned to | Source | Severity | Advisory | Reason |`
+                : `| Package | Pinned to | Source | Severity | Advisory |`;
+            const sep = hasReason
+                ? `| --- | --- | --- | --- | --- | --- |`
+                : `| --- | --- | --- | --- | --- |`;
+            lines.push(header);
+            lines.push(sep);
             for (const a of ok) {
                 const advCell = a.url && a.ids[0] ? `[${a.ids[0]}](${a.url})` : a.ids[0] ?? '';
-                lines.push(`| \`${a.name}\` | \`${a.applied ?? '?'}\` | ${a.severity} | ${advCell} |`);
+                const label = a.chain && a.chain.length > 1 ? a.chain.join(' › ') : a.name;
+                const sourceLabel = a.source === 'manual' ? '`--override`' : 'advisory';
+                const base = `| \`${label}\` | \`${a.applied ?? '?'}\` | ${sourceLabel} | ${a.severity} | ${advCell} |`;
+                lines.push(hasReason ? `${base} ${a.policyReason ?? ''} |` : base);
             }
             lines.push('');
         }
         if (failed.length > 0) {
             lines.push(`**Failed overrides** (rolled back):`);
             for (const a of failed) {
-                lines.push(`- \`${a.name}\` — ${a.reason ?? 'unknown'}`);
+                const label = a.chain && a.chain.length > 1 ? a.chain.join(' › ') : a.name;
+                lines.push(`- \`${label}\` — ${a.reason ?? 'unknown'}`);
             }
             lines.push('');
         }