@trustify-da/trustify-da-javascript-client 0.3.0-ea.c2f6c64 → 0.3.0-ea.c300d9f

package/dist/src/providers/rust_cargo.js

@@ -5,7 +5,7 @@ import { parse as parseToml } from 'smol-toml';
 import { getLicense } from '../license/license_utils.js';
 import Sbom from '../sbom.js';
 import { getCustom, getCustomPath, invokeCommand } from '../tools.js';
-export default { isSupported, validateLockFile, provideComponent, provideStack, readLicenseFromManifest };
+export default { isSupported, validateLockFile, provideComponent, provideStack, readLicenseFromManifest, packageManagerName() { return 'cargo'; } };
 /** @typedef {import('../provider').Provider} */
 /** @typedef {import('../provider').Provided} Provided */
 /**
@@ -71,15 +71,22 @@ function isSupported(manifestName) {
  * Read project license from Cargo.toml, with fallback to LICENSE file.
  * Supports the `license` field under `[package]` (single crate / workspace
  * with root) and under `[workspace.package]` (virtual workspaces).
+ * When a member crate uses `license = { workspace = true }`, the actual
+ * license is resolved from the workspace root Cargo.toml.
  * @param {string} manifestPath - path to Cargo.toml
+ * @param {object} [metadata] - cargo metadata output (needed for workspace license resolution)
  * @returns {string|null} SPDX identifier or null
  */
-function readLicenseFromManifest(manifestPath) {
+function readLicenseFromManifest(manifestPath, metadata) {
     let fromManifest = null;
     try {
         let content = fs.readFileSync(manifestPath, 'utf-8');
         let parsed = parseToml(content);
-        fromManifest = parsed.package?.license
+        let packageLicense = parsed.package?.license;
+        if (typeof packageLicense === 'object' && packageLicense?.workspace === true) {
+            packageLicense = resolveWorkspaceLicense(parsed, metadata);
+        }
+        fromManifest = packageLicense
             || parsed.workspace?.package?.license
             || null;
     }
@@ -89,30 +96,45 @@ function readLicenseFromManifest(manifestPath) {
     return getLicense(fromManifest, manifestPath);
 }
 /**
- * Validates that Cargo.lock exists in the manifest directory or in a parent
- * workspace root directory.  In Cargo workspaces the lock file always lives at
- * the workspace root, so when a member crate's Cargo.toml is provided we walk
- * up the directory tree looking for Cargo.lock (stopping when we find a
- * Cargo.toml that contains a [workspace] section, or when we reach the
- * filesystem root).
- * When TRUSTIFY_DA_WORKSPACE_DIR is provided (via env var or opts),
- * checks only that directory for Cargo.lock — no walk-up.
+ * Resolve a workspace-inherited license from the workspace root Cargo.toml.
+ * @param {object} parsed - the parsed member crate Cargo.toml
+ * @param {object} [metadata] - cargo metadata output with workspace_root
+ * @returns {string|null} resolved license string or null
+ */
+function resolveWorkspaceLicense(parsed, metadata) {
+    if (metadata?.workspace_root) {
+        let cargoTomlPath = path.join(metadata.workspace_root, 'Cargo.toml');
+        try {
+            let content = fs.readFileSync(cargoTomlPath, 'utf-8');
+            let workspaceParsed = parseToml(content);
+            return workspaceParsed.workspace?.package?.license || null;
+        }
+        catch (_) {
+            // fall through
+        }
+    }
+    return parsed.workspace?.package?.license || null;
+}
+/**
+ * Finds the directory containing Cargo.lock, honoring TRUSTIFY_DA_WORKSPACE_DIR.
+ * Walks up from manifestDir looking for Cargo.lock, stopping at workspace root or filesystem root.
  * @param {string} manifestDir - the directory where the manifest lies
  * @param {{TRUSTIFY_DA_WORKSPACE_DIR?: string}} [opts={}] - optional workspace root
- * @returns {boolean} true if Cargo.lock is found
+ * @returns {string|null} the directory path containing Cargo.lock, or null if not found
+ * @private
  */
-function validateLockFile(manifestDir, opts = {}) {
+function _findCargoLockDir(manifestDir, opts = {}) {
     const workspaceDir = getCustom('TRUSTIFY_DA_WORKSPACE_DIR', null, opts);
     if (workspaceDir) {
         const dir = path.resolve(workspaceDir);
-        return fs.existsSync(path.join(dir, 'Cargo.lock'));
+        return fs.existsSync(path.join(dir, 'Cargo.lock')) ? dir : null;
     }
     let dir = path.resolve(manifestDir);
     let parent = dir;
     do {
         dir = parent;
         if (fs.existsSync(path.join(dir, 'Cargo.lock'))) {
-            return true;
+            return dir;
         }
         // If this directory has a Cargo.toml with [workspace], the lock file
         // should have been here — stop searching.
@@ -121,7 +143,7 @@ function validateLockFile(manifestDir, opts = {}) {
             try {
                 let content = fs.readFileSync(cargoToml, 'utf-8');
                 if (/\[workspace\]/.test(content)) {
-                    return false;
+                    return null;
                 }
             }
             catch (_) {
@@ -130,7 +152,23 @@ function validateLockFile(manifestDir, opts = {}) {
         }
         parent = path.dirname(dir);
     } while (parent !== dir);
-    return false;
+    return null;
+}
+/**
+ * Validates that Cargo.lock exists in the manifest directory or in a parent
+ * workspace root directory.  In Cargo workspaces the lock file always lives at
+ * the workspace root, so when a member crate's Cargo.toml is provided we walk
+ * up the directory tree looking for Cargo.lock (stopping when we find a
+ * Cargo.toml that contains a [workspace] section, or when we reach the
+ * filesystem root).
+ * When TRUSTIFY_DA_WORKSPACE_DIR is provided (via env var or opts),
+ * checks only that directory for Cargo.lock — no walk-up.
+ * @param {string} manifestDir - the directory where the manifest lies
+ * @param {{TRUSTIFY_DA_WORKSPACE_DIR?: string}} [opts={}] - optional workspace root
+ * @returns {boolean} true if Cargo.lock is found
+ */
+function validateLockFile(manifestDir, opts = {}) {
+    return _findCargoLockDir(manifestDir, opts) !== null;
 }
 /**
  * Provide content and content type for Cargo stack analysis.
@@ -173,13 +211,14 @@ function getSBOM(manifest, opts = {}, includeTransitive) {
     let metadata = executeCargoMetadata(cargoBin, manifestDir);
     let ignoredDeps = getIgnoredDeps(manifest, metadata);
     let crateType = detectCrateType(metadata);
-    let license = readLicenseFromManifest(manifest);
+    let license = readLicenseFromManifest(manifest, metadata);
+    let hashMap = parseCargoLockHashes(manifestDir, opts);
     let sbom;
     if (crateType === CrateType.WORKSPACE_VIRTUAL) {
-        sbom = handleVirtualWorkspace(manifest, metadata, ignoredDeps, includeTransitive, opts, license);
+        sbom = handleVirtualWorkspace(manifest, metadata, ignoredDeps, includeTransitive, opts, license, hashMap);
     }
     else {
-        sbom = handleSingleCrate(metadata, ignoredDeps, includeTransitive, opts, license);
+        sbom = handleSingleCrate(metadata, ignoredDeps, includeTransitive, opts, license, hashMap);
     }
     return sbom;
 }
@@ -217,6 +256,34 @@ function executeCargoMetadata(cargoBin, manifestDir) {
         throw new Error('failed to execute cargo metadata', { cause: error });
     }
 }
+/**
+ * Parses Cargo.lock to extract SHA-256 checksums for each package.
+ * @param {string} manifestDir - directory containing Cargo.toml (Cargo.lock is searched upward)
+ * @param {{TRUSTIFY_DA_WORKSPACE_DIR?: string}} [opts={}] - optional workspace root
+ * @returns {Map<string, Array<{alg: string, content: string}>>} map of "name@version" to CycloneDX hashes
+ * @private
+ */
+function parseCargoLockHashes(manifestDir, opts = {}) {
+    let hashMap = new Map();
+    let lockDir = _findCargoLockDir(manifestDir, opts);
+    if (!lockDir) {
+        return hashMap;
+    }
+    let lockPath = path.join(lockDir, 'Cargo.lock');
+    try {
+        let content = fs.readFileSync(lockPath, 'utf-8');
+        let parsed = parseToml(content);
+        for (let pkg of (parsed.package || [])) {
+            if (pkg.name && pkg.version && pkg.checksum) {
+                hashMap.set(`${pkg.name}@${pkg.version}`, [{ alg: 'SHA-256', content: pkg.checksum }]);
+            }
+        }
+    }
+    catch (error) {
+        console.warn(`Failed to parse Cargo.lock at ${lockPath} for hashes: ${error.message}. SBOM will be generated without hashes.`);
+    }
+    return hashMap;
+}
 /**
  * Detects the type of Cargo project from metadata.
  * @param {object} metadata - parsed cargo metadata
@@ -248,7 +315,7 @@ function detectCrateType(metadata) {
  * @returns {string} SBOM json string
  * @private
  */
-function handleSingleCrate(metadata, ignoredDeps, includeTransitive, opts, license) {
+function handleSingleCrate(metadata, ignoredDeps, includeTransitive, opts, license, hashMap) {
     let rootPackageId = metadata.resolve.root;
     let rootPackage = findPackageById(metadata, rootPackageId);
     let rootPurl = toPurl(rootPackage.name, rootPackage.version);
@@ -259,10 +326,10 @@ function handleSingleCrate(metadata, ignoredDeps, includeTransitive, opts, licen
         return sbom.getAsJsonString(opts);
     }
     if (includeTransitive) {
-        addTransitiveDeps(sbom, metadata, rootPackageId, ignoredDeps, new Set(), rootPurl);
+        addTransitiveDeps(sbom, metadata, rootPackageId, ignoredDeps, new Set(), hashMap, rootPurl);
     }
     else {
-        addDirectDeps(sbom, metadata, rootPackageId, rootPurl, ignoredDeps);
+        addDirectDeps(sbom, metadata, rootPackageId, rootPurl, ignoredDeps, hashMap);
     }
     return sbom.getAsJsonString(opts);
 }
@@ -288,7 +355,7 @@ function handleSingleCrate(metadata, ignoredDeps, includeTransitive, opts, licen
  * @returns {string} SBOM json string
  * @private
  */
-function handleVirtualWorkspace(manifest, metadata, ignoredDeps, includeTransitive, opts, license) {
+function handleVirtualWorkspace(manifest, metadata, ignoredDeps, includeTransitive, opts, license, hashMap) {
     let workspaceRoot = metadata.workspace_root;
     let rootName = path.basename(workspaceRoot);
     let workspaceVersion = getWorkspaceVersion(metadata);
@@ -296,7 +363,6 @@ function handleVirtualWorkspace(manifest, metadata, ignoredDeps, includeTransiti
     let sbom = new Sbom();
     sbom.addRoot(rootPurl, license);
     if (includeTransitive) {
-        // Stack analysis: walk all members and their full dependency trees
         let workspaceMembers = metadata.workspace_members || [];
         for (let memberId of workspaceMembers) {
             let memberPackage = findPackageById(metadata, memberId);
@@ -307,11 +373,10 @@ function handleVirtualWorkspace(manifest, metadata, ignoredDeps, includeTransiti
                 ? toPathDepPurl(memberPackage.name, memberPackage.version)
                 : toPurl(memberPackage.name, memberPackage.version);
             sbom.addDependency(rootPurl, memberPurl);
-            addTransitiveDeps(sbom, metadata, memberId, ignoredDeps, new Set(), memberPurl);
+            addTransitiveDeps(sbom, metadata, memberId, ignoredDeps, new Set(), hashMap, memberPurl);
         }
     }
     else {
-        // Component analysis: only [workspace.dependencies] from root Cargo.toml
         let workspaceDeps = getWorkspaceDepsFromManifest(manifest);
         for (let depName of workspaceDeps) {
             if (isDepIgnored(depName, ignoredDeps)) {
@@ -328,7 +393,8 @@ function handleVirtualWorkspace(manifest, metadata, ignoredDeps, includeTransiti
             let depPurl = pkg.source == null
                 ? toPathDepPurl(pkg.name, pkg.version)
                 : toPurl(pkg.name, pkg.version);
-            sbom.addDependency(rootPurl, depPurl);
+            let hashes = hashMap.get(`${pkg.name}@${pkg.version}`);
+            sbom.addDependency(rootPurl, depPurl, undefined, hashes);
         }
     }
     return sbom.getAsJsonString(opts);
@@ -347,7 +413,7 @@ function handleVirtualWorkspace(manifest, metadata, ignoredDeps, includeTransiti
  *   so callers can ensure it matches the purl already added to the SBOM
  * @private
  */
-function addTransitiveDeps(sbom, metadata, packageId, ignoredDeps, visited, startingPurl) {
+function addTransitiveDeps(sbom, metadata, packageId, ignoredDeps, visited, hashMap, startingPurl) {
     if (visited.has(packageId)) {
         return;
     }
@@ -375,8 +441,9 @@ function addTransitiveDeps(sbom, metadata, packageId, ignoredDeps, visited, star
         let depPurl = depPackage.source == null
             ? toPathDepPurl(depPackage.name, depPackage.version)
             : toPurl(depPackage.name, depPackage.version);
-        sbom.addDependency(sourcePurl, depPurl);
-        addTransitiveDeps(sbom, metadata, depId, ignoredDeps, visited);
+        let hashes = hashMap.get(`${depPackage.name}@${depPackage.version}`);
+        sbom.addDependency(sourcePurl, depPurl, undefined, hashes);
+        addTransitiveDeps(sbom, metadata, depId, ignoredDeps, visited, hashMap);
     }
 }
 /**
@@ -389,7 +456,7 @@ function addTransitiveDeps(sbom, metadata, packageId, ignoredDeps, visited, star
  * @param {Set<string>} ignoredDeps - set of ignored dependency names
  * @private
  */
-function addDirectDeps(sbom, metadata, packageId, parentPurl, ignoredDeps) {
+function addDirectDeps(sbom, metadata, packageId, parentPurl, ignoredDeps, hashMap) {
     let resolveNode = findResolveNode(metadata, packageId);
     if (!resolveNode) {
         return;
@@ -406,7 +473,8 @@ function addDirectDeps(sbom, metadata, packageId, parentPurl, ignoredDeps) {
         let depPurl = depPackage.source == null
             ? toPathDepPurl(depPackage.name, depPackage.version)
             : toPurl(depPackage.name, depPackage.version);
-        sbom.addDependency(parentPurl, depPurl);
+        let hashes = hashMap.get(`${depPackage.name}@${depPackage.version}`);
+        sbom.addDependency(parentPurl, depPurl, undefined, hashes);
     }
 }
 /**

package/dist/src/remediate.d.ts

@@ -0,0 +1,120 @@
+/**
+ * Resolves a target path to the supported manifest files it contains: the single file
+ * if `targetPath` is a supported manifest, or every supported manifest discovered
+ * recursively if it's a directory. This is the single source of truth for what
+ * `runRemediation` will scan, so callers (e.g. the CLI) can reuse it to tell
+ * "no manifests here" apart from "manifests, but nothing to fix".
+ * @param {string} targetPath - path to a manifest file or directory
+ * @returns {string[]} absolute paths to supported manifests (empty for an empty directory)
+ * @throws if the path does not exist, or is a file of an unsupported manifest type
+ */
+export function findManifests(targetPath: string): string[];
+/**
+ * Orchestrates the full remediation pipeline for a single manifest or directory:
+ * discover manifests → scan via DA backend → extract remediations → apply or preview.
+ *
+ * @param {string} targetPath - path to a manifest file or directory
+ * @param {object} [options]
+ * @param {boolean} [options.dryRun=false] - preview changes without modifying files (applies by default)
+ * @param {string} [options.providers] - comma-separated provider list
+ * @param {string} [options.sources] - comma-separated source list
+ * @param {string} [options.backendUrl] - Trustify DA backend URL
+ * @param {boolean} [options.perDependencyChanges=false] - when true, each remediation is populated with
+ *   a `changes` array describing the isolated, single-dependency edit (see {@link DependencyFix}). This lets
+ *   callers create one commit/PR per dependency without attributing diff hunks themselves.
+ * @returns {Promise<{exitCode: number, output: string, remediations: Remediation[], manifests: string[], appliedFiles: string[]}>}
+ *   exitCode is 2 for a dry-run that found remediations (nothing written), 0 otherwise. `remediations`
+ *   is the structured, per-manifest list of applicable updates — each entry carries the originating
+ *   manifest path(s) in `files` so callers can group and create per-dependency changes. `appliedFiles`
+ *   lists only the manifests actually written to disk (empty on a dry-run), so callers can report a
+ *   truthful "updated N files" count without conflating "had remediations" with "was written".
+ */
+export function runRemediation(targetPath: string, options?: {
+    dryRun?: boolean | undefined;
+    providers?: string | undefined;
+    sources?: string | undefined;
+    backendUrl?: string | undefined;
+    perDependencyChanges?: boolean | undefined;
+}): Promise<{
+    exitCode: number;
+    output: string;
+    remediations: Remediation[];
+    manifests: string[];
+    appliedFiles: string[];
+}>;
+/**
+ * A single version change requested from an updater: bump `groupId:artifactId` to `newVersion`.
+ * The input side of every updater; each updater's output side (its `applied` entries) is its own
+ * type — see {@link AppliedChange}.
+ */
+export type VersionChangeRequest = {
+    groupId: string;
+    artifactId: string;
+    newVersion: string;
+};
+/**
+ * One entry from an updater's `applied` list, describing where and how a version was changed.
+ * Owned by the updater layer: the union of each updater's applied-entry shape. `changeKey`
+ * (per {@link ManifestType}) turns one of these into a stable edit-site identifier.
+ */
+export type AppliedChange = import("./updaters/maven_updater.js").MavenAppliedChange | import("./updaters/toml_updater.js").TomlAppliedChange;
+/**
+ * The result of running an updater over a manifest's raw content.
+ */
+export type UpdaterResult = {
+    content: string;
+    applied: AppliedChange[];
+    skipped: Array<{
+        groupId: string;
+        artifactId: string;
+        newVersion: string;
+        reason: string;
+    }>;
+};
+/**
+ * A supported manifest type and the operations that act on it.
+ * `changeKey` builds a stable edit-site key from a single `applied` entry, so callers can detect
+ * inseparable remediations (same key => same commit/PR).
+ */
+export type ManifestType = {
+    test: (basename: string) => boolean;
+    updater: (content: string, versionChanges: VersionChangeRequest[]) => UpdaterResult;
+    label: ("maven" | "toml");
+    changeKey: (manifestPath: string, applied: AppliedChange) => string;
+};
+/**
+ * An isolated, single-dependency edit to one manifest file.
+ * - `after` is the *original* manifest content with only this dependency's fix applied, so a caller
+ *   can create an isolated commit by writing `after` to `path` on a branch cut from the base.
+ * - `changeKey` is a stable identifier for the underlying edit site. Two remediations that share a
+ *   `changeKey` are inseparable (e.g. two Maven deps whose versions resolve to the same `${property}`,
+ *   or two Gradle libraries sharing one `version.ref`) and MUST land in the same commit/PR — the
+ *   caller should union their CVEs/advisories.
+ */
+export type DependencyFix = {
+    path: string;
+    after: string;
+    changeKey: string;
+};
+/**
+ * A single applicable remediation, as produced by `extractRemediations` and enriched by
+ * `runRemediation` with the originating manifest path(s) and (optionally) per-dependency changes.
+ */
+export type Remediation = {
+    purl: string;
+    groupId: string;
+    artifactId: string;
+    currentVersion: string;
+    fixedInVersion: string;
+    fixedInPurl: string;
+    provider: string;
+    source: string;
+    advisories: Array<{
+        id: string;
+        url: string;
+    }>;
+    severity: string;
+    cves: string[];
+    files: string[];
+    changes?: DependencyFix[];
+};

package/dist/src/remediate.js

@@ -0,0 +1,253 @@
+import fs from 'node:fs';
+import path from 'node:path';
+import analysis from './analysis.js';
+import { availableProviders, match } from './provider.js';
+import { extractRemediations } from './remediation.js';
+import { mavenChangeKey, updateMavenVersions } from './updaters/maven_updater.js';
+import { tomlChangeKey, updateTomlVersions } from './updaters/toml_updater.js';
+import { selectTrustifyDABackend } from './index.js';
+// Mirrors DEFAULT_WORKSPACE_DISCOVERY_IGNORE in workspace.js
+const SKIP_DIRS = new Set(['node_modules', '.git']);
+/**
+ * A single version change requested from an updater: bump `groupId:artifactId` to `newVersion`.
+ * The input side of every updater; each updater's output side (its `applied` entries) is its own
+ * type — see {@link AppliedChange}.
+ * @typedef {{groupId: string, artifactId: string, newVersion: string}} VersionChangeRequest
+ */
+/**
+ * One entry from an updater's `applied` list, describing where and how a version was changed.
+ * Owned by the updater layer: the union of each updater's applied-entry shape. `changeKey`
+ * (per {@link ManifestType}) turns one of these into a stable edit-site identifier.
+ * @typedef {import('./updaters/maven_updater.js').MavenAppliedChange
+ *   | import('./updaters/toml_updater.js').TomlAppliedChange} AppliedChange
+ */
+/**
+ * The result of running an updater over a manifest's raw content.
+ * @typedef {{content: string, applied: AppliedChange[], skipped: Array<{groupId: string, artifactId: string, newVersion: string, reason: string}>}} UpdaterResult
+ */
+/**
+ * A supported manifest type and the operations that act on it.
+ * `changeKey` builds a stable edit-site key from a single `applied` entry, so callers can detect
+ * inseparable remediations (same key => same commit/PR).
+ * @typedef {{
+ *   test: (basename: string) => boolean,
+ *   updater: (content: string, versionChanges: VersionChangeRequest[]) => UpdaterResult,
+ *   label: ('maven'|'toml'),
+ *   changeKey: (manifestPath: string, applied: AppliedChange) => string
+ * }} ManifestType
+ */
+/**
+ * An isolated, single-dependency edit to one manifest file.
+ * - `after` is the *original* manifest content with only this dependency's fix applied, so a caller
+ *   can create an isolated commit by writing `after` to `path` on a branch cut from the base.
+ * - `changeKey` is a stable identifier for the underlying edit site. Two remediations that share a
+ *   `changeKey` are inseparable (e.g. two Maven deps whose versions resolve to the same `${property}`,
+ *   or two Gradle libraries sharing one `version.ref`) and MUST land in the same commit/PR — the
+ *   caller should union their CVEs/advisories.
+ * @typedef {{ path: string, after: string, changeKey: string }} DependencyFix
+ */
+/**
+ * A single applicable remediation, as produced by `extractRemediations` and enriched by
+ * `runRemediation` with the originating manifest path(s) and (optionally) per-dependency changes.
+ * @typedef {{
+ *   purl: string,
+ *   groupId: string,
+ *   artifactId: string,
+ *   currentVersion: string,
+ *   fixedInVersion: string,
+ *   fixedInPurl: string,
+ *   provider: string,
+ *   source: string,
+ *   advisories: Array<{id: string, url: string}>,
+ *   severity: string,
+ *   cves: string[],
+ *   files: string[],
+ *   changes?: DependencyFix[]
+ * }} Remediation
+ */
+/** @type {ManifestType[]} */
+const MANIFEST_TYPES = [
+    {
+        test: (basename) => basename === 'pom.xml',
+        updater: updateMavenVersions,
+        label: 'maven',
+        changeKey: mavenChangeKey
+    },
+    {
+        test: (basename) => basename.endsWith('.versions.toml') || basename === 'libs.versions.toml',
+        updater: updateTomlVersions,
+        label: 'toml',
+        changeKey: tomlChangeKey
+    },
+];
+/**
+ * Returns the manifest type descriptor for a given filename, or null if unsupported.
+ * @param {string} basename - the file name to check
+ * @returns {ManifestType|null}
+ */
+function getManifestType(basename) {
+    return MANIFEST_TYPES.find(t => t.test(basename)) || null;
+}
+/**
+ * Resolves a target path to the supported manifest files it contains: the single file
+ * if `targetPath` is a supported manifest, or every supported manifest discovered
+ * recursively if it's a directory. This is the single source of truth for what
+ * `runRemediation` will scan, so callers (e.g. the CLI) can reuse it to tell
+ * "no manifests here" apart from "manifests, but nothing to fix".
+ * @param {string} targetPath - path to a manifest file or directory
+ * @returns {string[]} absolute paths to supported manifests (empty for an empty directory)
+ * @throws if the path does not exist, or is a file of an unsupported manifest type
+ */
+export function findManifests(targetPath) {
+    const resolvedPath = path.resolve(targetPath);
+    let stat;
+    try {
+        stat = fs.statSync(resolvedPath);
+    }
+    catch {
+        throw new Error(`Path not found: ${resolvedPath}`);
+    }
+    // A single file must itself be a supported manifest.
+    if (!stat.isDirectory()) {
+        const basename = path.basename(resolvedPath);
+        if (!getManifestType(basename)) {
+            throw new Error(`Unsupported manifest type: ${basename}`);
+        }
+        return [resolvedPath];
+    }
+    // A directory yields every supported manifest found recursively beneath it.
+    const manifests = [];
+    function walk(dir) {
+        for (const entry of fs.readdirSync(dir, { withFileTypes: true })) {
+            if (SKIP_DIRS.has(entry.name)) {
+                continue;
+            }
+            const fullPath = path.join(dir, entry.name);
+            if (entry.isDirectory()) {
+                walk(fullPath);
+            }
+            else if (getManifestType(entry.name)) {
+                manifests.push(fullPath);
+            }
+        }
+    }
+    walk(resolvedPath);
+    return manifests;
+}
+/**
+ * Orchestrates the full remediation pipeline for a single manifest or directory:
+ * discover manifests → scan via DA backend → extract remediations → apply or preview.
+ *
+ * @param {string} targetPath - path to a manifest file or directory
+ * @param {object} [options]
+ * @param {boolean} [options.dryRun=false] - preview changes without modifying files (applies by default)
+ * @param {string} [options.providers] - comma-separated provider list
+ * @param {string} [options.sources] - comma-separated source list
+ * @param {string} [options.backendUrl] - Trustify DA backend URL
+ * @param {boolean} [options.perDependencyChanges=false] - when true, each remediation is populated with
+ *   a `changes` array describing the isolated, single-dependency edit (see {@link DependencyFix}). This lets
+ *   callers create one commit/PR per dependency without attributing diff hunks themselves.
+ * @returns {Promise<{exitCode: number, output: string, remediations: Remediation[], manifests: string[], appliedFiles: string[]}>}
+ *   exitCode is 2 for a dry-run that found remediations (nothing written), 0 otherwise. `remediations`
+ *   is the structured, per-manifest list of applicable updates — each entry carries the originating
+ *   manifest path(s) in `files` so callers can group and create per-dependency changes. `appliedFiles`
+ *   lists only the manifests actually written to disk (empty on a dry-run), so callers can report a
+ *   truthful "updated N files" count without conflating "had remediations" with "was written".
+ */
+export async function runRemediation(targetPath, options = {}) {
+    const { dryRun = false, providers, sources, perDependencyChanges = false, backendUrl } = options;
+    const manifestPaths = findManifests(targetPath);
+    if (manifestPaths.length === 0) {
+        return { exitCode: 0, remediations: [], manifests: manifestPaths, appliedFiles: [] };
+    }
+    const opts = {};
+    if (backendUrl !== undefined) {
+        opts.TRUSTIFY_DA_BACKEND_URL = backendUrl;
+    }
+    if (providers !== undefined) {
+        opts.TRUSTIFY_DA_PROVIDERS = providers;
+    }
+    if (sources !== undefined) {
+        opts.TRUSTIFY_DA_SOURCES = sources;
+    }
+    const url = selectTrustifyDABackend(opts);
+    const allRemediations = [];
+    const appliedFiles = [];
+    for (const manifestPath of manifestPaths) {
+        const basename = path.basename(manifestPath);
+        const manifestType = getManifestType(basename);
+        if (!manifestType) {
+            continue;
+        }
+        let provider;
+        try {
+            provider = match(manifestPath, availableProviders, opts);
+        }
+        catch {
+            continue;
+        }
+        const analysisReport = await analysis.requestStack(provider, manifestPath, url, false, opts);
+        const remediations = extractRemediations(analysisReport, {
+            providerPriority: providers ? providers.split(',').map(p => p.trim()).filter(Boolean) : undefined,
+        });
+        if (remediations.length === 0) {
+            continue;
+        }
+        // Tag each remediation with the manifest it came from so callers can group
+        // changes per dependency across a multi-manifest workspace.
+        for (const remediation of remediations) {
+            remediation.files = [manifestPath];
+        }
+        // Read the pristine manifest once. Both the atomic apply and the per-dependency
+        // change computation must diff against the *original* content.
+        const needsContent = perDependencyChanges || !dryRun;
+        const originalContent = needsContent ? fs.readFileSync(manifestPath, 'utf-8') : null;
+        if (perDependencyChanges) {
+            // With per-dependency changes every returned remediation must carry an isolated
+            // edit. A dependency the updater cannot locate in this manifest — e.g. a vulnerable
+            // *transitive* dependency surfaced by analysis but not declared here — yields no
+            // applied change, so it is dropped rather than returned with an absent `changes`
+            // array (which would crash callers that iterate `remediation.changes` to build PRs).
+            const applicable = [];
+            for (const remediation of remediations) {
+                const isolated = manifestType.updater(originalContent, [{
+                        groupId: remediation.groupId,
+                        artifactId: remediation.artifactId,
+                        newVersion: remediation.fixedInVersion,
+                    }]);
+                if (isolated.applied.length === 0) {
+                    continue;
+                }
+                remediation.changes = [{
+                        path: manifestPath,
+                        after: isolated.content,
+                        changeKey: manifestType.changeKey(manifestPath, isolated.applied[0])
+                    }];
+                applicable.push(remediation);
+            }
+            allRemediations.push(...applicable);
+        }
+        else {
+            allRemediations.push(...remediations);
+        }
+        if (!dryRun) {
+            // Disk receives the union of every dependency's fix. When
+            // perDependencyChanges is also set, each remediation's `changes[].after`
+            // deliberately stays isolated (single-dep) for branch-per-dep workflows.
+            const result = manifestType.updater(originalContent, remediations.map(r => ({
+                groupId: r.groupId,
+                artifactId: r.artifactId,
+                newVersion: r.fixedInVersion,
+            })));
+            if (result.applied.length > 0) {
+                fs.writeFileSync(manifestPath, result.content, 'utf-8');
+                appliedFiles.push(manifestPath);
+            }
+        }
+    }
+    if (allRemediations.length === 0) {
+        return { exitCode: 0, remediations: [], manifests: manifestPaths, appliedFiles };
+    }
+    // Dry-run signals "changes available but not written" via exit code 2.
+    return { exitCode: dryRun ? 2 : 0, remediations: allRemediations, manifests: manifestPaths, appliedFiles };
+}