@vibe-agent-toolkit/agent-skills 0.1.38 → 0.1.39-rc.10

package/dist/post-build-checks.js

@@ -4,11 +4,12 @@
  * Run after packageSkill() completes — all files are copied, all links rewritten.
  * Detects unreferenced files and broken links in the packaged output.
  */
-import { existsSync, readdirSync } from 'node:fs';
+import { existsSync, readdirSync, statSync } from 'node:fs';
 import { readFile } from 'node:fs/promises';
 import { dirname } from 'node:path';
+import { parseHtml } from '@vibe-agent-toolkit/resources';
 import { safePath, toForwardSlash } from '@vibe-agent-toolkit/utils';
-import { CODE_REGISTRY } from './validators/code-registry.js';
+import { evaluate, makeRuleContext, materializeIssue } from './validators/rule-engine/index.js';
 /**
  * Regex matching markdown inline links: [text](href).
  * Negated character classes [^\]\\] and [^)] are non-backtracking by design.
@@ -76,38 +77,105 @@ function extractLocalLinks(content) {
     return links;
 }
 /**
- * Walk the markdown link graph starting at SKILL.md and return the set of
+ * Extract local file hrefs from a content file — markdown or HTML.
+ *
+ * For markdown: regex-matches `[text](href)` links, skipping code blocks.
+ * For HTML/HTM: uses `parseHtml` (parse5-based) and returns `local_file` hrefs only.
+ * Fragments are stripped from all returned hrefs.
+ */
+async function extractLocalHrefs(filePath) {
+    if (filePath.endsWith('.html') || filePath.endsWith('.htm')) {
+        const result = await parseHtml(filePath);
+        return result.links
+            .filter(link => link.type === 'local_file')
+            .map(link => {
+            const [withoutFragment] = link.href.split('#');
+            return withoutFragment ?? '';
+        })
+            .filter(href => href.length > 0);
+    }
+    // Markdown: read content and regex-match
+    // eslint-disable-next-line security/detect-non-literal-fs-filename -- filePath from walkDir
+    const content = await readFile(filePath, 'utf-8');
+    return extractLocalLinks(content);
+}
+/**
+ * Check hrefs from a content file against allFileSet and return PACKAGED_BROKEN_LINK
+ * issues for any that don't resolve to a file in the packaged output.
+ *
+ * Shared by markdown and HTML broken-link checks to eliminate duplicate resolve/emit logic.
+ */
+function collectBrokenLinkIssues(sourceFile, hrefs, allFileSet, outputDir) {
+    const issues = [];
+    const relativeSourcePath = toForwardSlash(safePath.relative(outputDir, sourceFile));
+    for (const href of hrefs) {
+        const resolved = toForwardSlash(safePath.resolve(dirname(sourceFile), href));
+        if (!allFileSet.has(resolved)) {
+            // A navigational directory link (href ending in `/`, classified `local_directory`)
+            // is a valid target if the directory itself exists on disk — walkDir populates
+            // allFileSet with FILES only, so directory paths are never in the set.
+            // Note: a NO-SLASH link (`[Concepts](concepts)`, classified `local_file`) that
+            // happens to resolve to a directory is a different case — it matches the
+            // link-rewrite bundled-link rule (skill-packager.ts buildRewriteRules) and
+            // renders with an undefined `link.resource.*`. Fixing that is the
+            // link-rewrite engine's job, tracked under #129 (slice 3, built-path
+            // unification). The slash form (`concepts/`, `local_directory`) survives
+            // rewrite verbatim and is the realistic navigational case this guard covers.
+            // eslint-disable-next-line security/detect-non-literal-fs-filename -- resolved is a normalized path from a validated output directory
+            const isExistingDirectory = statSync(resolved, { throwIfNoEntry: false })?.isDirectory() === true;
+            if (isExistingDirectory) {
+                continue;
+            }
+            // Built-path edge extraction: a link whose target is absent from the
+            // packaged output. The engine resolves this to PACKAGED_BROKEN_LINK
+            // (a link-rewriter bug) rather than LINK_MISSING_TARGET via phase: 'built'.
+            const code = evaluate(makeRuleContext({ subject: 'edge', phase: 'built', existsAtSource: false }));
+            if (code !== null) {
+                issues.push(materializeIssue(code, {
+                    location: relativeSourcePath,
+                    detail: `link: ${href} from ${relativeSourcePath}`,
+                }));
+            }
+        }
+    }
+    return issues;
+}
+/**
+ * Walk the markdown and HTML link graph starting at SKILL.md and return the set of
  * referenced file paths (normalized to forward slashes).
  *
- * SKILL.md itself is always included as the root.
+ * SKILL.md itself is always included as the root. Traversal follows `.md`, `.html`,
+ * and `.htm` links transitively so an HTML file referenced only by another HTML file
+ * is not reported as unreferenced.
  */
 async function collectReferencedPaths(outputDir, allFileSet) {
     const referenced = new Set();
     const skillMdPath = safePath.join(outputDir, 'SKILL.md');
-    const mdQueue = [skillMdPath];
+    const fileQueue = [skillMdPath];
     const visited = new Set();
     // SKILL.md itself is the root — always referenced
     referenced.add(toForwardSlash(skillMdPath));
-    while (mdQueue.length > 0) {
-        const mdFile = mdQueue.shift();
-        if (!mdFile)
+    while (fileQueue.length > 0) {
+        const filePath = fileQueue.shift();
+        if (!filePath)
             break;
-        const normalized = toForwardSlash(mdFile);
+        const normalized = toForwardSlash(filePath);
         if (visited.has(normalized))
             continue;
         visited.add(normalized);
-        // eslint-disable-next-line security/detect-non-literal-fs-filename -- mdFile from walkDir output
-        if (!existsSync(mdFile))
+        // eslint-disable-next-line security/detect-non-literal-fs-filename -- filePath from walkDir output
+        if (!existsSync(filePath))
             continue;
-        // eslint-disable-next-line security/detect-non-literal-fs-filename -- mdFile validated above
-        const content = await readFile(mdFile, 'utf-8');
-        const links = extractLocalLinks(content);
-        for (const href of links) {
-            const resolved = toForwardSlash(safePath.resolve(dirname(mdFile), href));
+        const hrefs = await extractLocalHrefs(filePath);
+        for (const href of hrefs) {
+            const resolved = toForwardSlash(safePath.resolve(dirname(filePath), href));
             referenced.add(resolved);
-            // If it's a markdown file in the output, traverse it transitively
-            if (resolved.endsWith('.md') && allFileSet.has(resolved) && !visited.has(resolved)) {
-                mdQueue.push(resolved);
+            // Traverse .md, .html, and .htm files transitively
+            const isTraversable = (resolved.endsWith('.md') || resolved.endsWith('.html') || resolved.endsWith('.htm')) &&
+                allFileSet.has(resolved) &&
+                !visited.has(resolved);
+            if (isTraversable) {
+                fileQueue.push(resolved);
             }
         }
     }
@@ -115,22 +183,22 @@ async function collectReferencedPaths(outputDir, allFileSet) {
 }
 /**
  * Record packaged files whose output-relative path appears anywhere in any
- * packaged markdown — inside code blocks (`` ```bash\nnode scripts/cli.mjs `` ``),
- * inline code spans, or prose — as "documented" references.
+ * packaged content file (markdown or HTML) — inside code blocks, inline code
+ * spans, or prose — as "documented" references.
  *
  * A file that a skill author chose to bundle but never documents is the real
  * problem this check exists to catch; documentation by code-block invocation
  * is still documentation. By contrast, `collectReferencedPaths` is intentionally
- * strict (only `[text](href)` links) because it also walks the transitive link
+ * strict (only formal link syntax) because it also walks the transitive link
  * graph, which would be unbounded if we followed substring hits.
  */
-async function addMentionReferences(outputDir, referenced, candidates, mdFiles) {
-    if (candidates.length === 0 || mdFiles.length === 0) {
+async function addMentionReferences(outputDir, referenced, candidates, contentFiles) {
+    if (candidates.length === 0 || contentFiles.length === 0) {
         return;
     }
     const contents = await Promise.all(
-    // eslint-disable-next-line security/detect-non-literal-fs-filename -- mdFile from walkDir
-    mdFiles.map(f => readFile(f, 'utf-8')));
+    // eslint-disable-next-line security/detect-non-literal-fs-filename -- contentFile from walkDir
+    contentFiles.map(f => readFile(f, 'utf-8')));
     const haystack = contents.join('\n');
     for (const candidate of candidates) {
         const relativePath = toForwardSlash(safePath.relative(outputDir, candidate));
@@ -140,68 +208,58 @@ async function addMentionReferences(outputDir, referenced, candidates, mdFiles)
     }
 }
 /**
- * Check that every file in the packaged output is referenced from some markdown file.
+ * Check that every file in the packaged output is referenced from some markdown or HTML file.
  *
  * Two-pass detection:
- * 1. Walk `[text](href)` link graph from SKILL.md (strict, transitive).
+ * 1. Walk formal link graph from SKILL.md (strict, transitive, covers .md and .html/.htm).
  * 2. For files not covered by pass 1, check whether their output-relative path
- *    is mentioned anywhere in packaged markdown (code blocks, prose, etc.).
+ *    is mentioned anywhere in packaged content files (markdown or HTML).
  *    Authors often document CLI scripts via invocation examples rather than
- *    markdown links, and that counts as documented.
+ *    formal links, and that counts as documented.
  */
 export async function checkUnreferencedFiles(outputDir) {
     const allFiles = walkDir(outputDir);
     const allFileSet = new Set(allFiles.map(f => toForwardSlash(f)));
     const referenced = await collectReferencedPaths(outputDir, allFileSet);
-    // Second pass: treat any path mention in packaged markdown as documentation.
+    // Second pass: treat any path mention in packaged content files as documentation.
     const candidates = allFiles.filter(f => !referenced.has(toForwardSlash(f)));
-    const mdFiles = allFiles.filter(f => f.endsWith('.md'));
-    await addMentionReferences(outputDir, referenced, candidates, mdFiles);
+    const contentFiles = allFiles.filter(f => f.endsWith('.md') || f.endsWith('.html') || f.endsWith('.htm'));
+    await addMentionReferences(outputDir, referenced, candidates, contentFiles);
     // Find unreferenced files
     const issues = [];
     for (const file of allFiles) {
         const normalized = toForwardSlash(file);
         if (!referenced.has(normalized)) {
             const relativePath = toForwardSlash(safePath.relative(outputDir, file));
-            issues.push({
-                severity: CODE_REGISTRY.PACKAGED_UNREFERENCED_FILE.defaultSeverity,
-                code: 'PACKAGED_UNREFERENCED_FILE',
-                message: `Packaged file not referenced from any markdown: ${relativePath}`,
-                location: relativePath,
-                fix: CODE_REGISTRY.PACKAGED_UNREFERENCED_FILE.fix,
-                reference: CODE_REGISTRY.PACKAGED_UNREFERENCED_FILE.reference,
-            });
+            // Built-path file extraction: a packaged file reachable by neither link
+            // nor mention nor files: declaration. The engine resolves this to
+            // PACKAGED_UNREFERENCED_FILE for a skill-bundled copy at the built phase.
+            const code = evaluate(makeRuleContext({
+                subject: 'file',
+                phase: 'built',
+                copyRole: 'skill-bundled',
+                reachableFromSkillMd: false,
+                referencedHow: 'none',
+            }));
+            if (code !== null) {
+                issues.push(materializeIssue(code, { location: relativePath, detail: relativePath }));
+            }
         }
     }
     return issues;
 }
 /**
- * Check that every local file link in packaged markdown files resolves to a file
+ * Check that every local file link in packaged markdown and HTML files resolves to a file
  * that exists in the packaged output.
  */
 export async function checkBrokenPackagedLinks(outputDir) {
     const allFiles = walkDir(outputDir);
-    const mdFiles = allFiles.filter(f => f.endsWith('.md'));
+    const linkableFiles = allFiles.filter(f => f.endsWith('.md') || f.endsWith('.html') || f.endsWith('.htm'));
     const allFileSet = new Set(allFiles.map(f => toForwardSlash(f)));
     const issues = [];
-    for (const mdFile of mdFiles) {
-        // eslint-disable-next-line security/detect-non-literal-fs-filename -- mdFile from walkDir
-        const content = await readFile(mdFile, 'utf-8');
-        const links = extractLocalLinks(content);
-        const relativeMdPath = toForwardSlash(safePath.relative(outputDir, mdFile));
-        for (const href of links) {
-            const resolved = toForwardSlash(safePath.resolve(dirname(mdFile), href));
-            if (!allFileSet.has(resolved)) {
-                issues.push({
-                    severity: CODE_REGISTRY.PACKAGED_BROKEN_LINK.defaultSeverity,
-                    code: 'PACKAGED_BROKEN_LINK',
-                    message: `Broken link in packaged output: ${href} (from ${relativeMdPath})`,
-                    location: relativeMdPath,
-                    fix: CODE_REGISTRY.PACKAGED_BROKEN_LINK.fix,
-                    reference: CODE_REGISTRY.PACKAGED_BROKEN_LINK.reference,
-                });
-            }
-        }
+    for (const sourceFile of linkableFiles) {
+        const hrefs = await extractLocalHrefs(sourceFile);
+        issues.push(...collectBrokenLinkIssues(sourceFile, hrefs, allFileSet, outputDir));
     }
     return issues;
 }

package/dist/post-build-checks.js.map

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package/dist/schemas/installed-plugins-registry.d.ts

@@ -11,16 +11,16 @@ declare const PluginInstallationSchema: z.ZodObject<{
     gitCommitSha: z.ZodOptional<z.ZodString>;
     isLocal: z.ZodBoolean;
 }, "strict", z.ZodTypeAny, {
-    version: string;
     scope: "user" | "system";
+    version: string;
     installPath: string;
     installedAt: string;
     lastUpdated: string;
     isLocal: boolean;
     gitCommitSha?: string | undefined;
 }, {
-    version: string;
     scope: "user" | "system";
+    version: string;
     installPath: string;
     installedAt: string;
     lastUpdated: string;
@@ -46,16 +46,16 @@ export declare const InstalledPluginsRegistrySchema: z.ZodObject<{
         gitCommitSha: z.ZodOptional<z.ZodString>;
         isLocal: z.ZodBoolean;
     }, "strict", z.ZodTypeAny, {
-        version: string;
         scope: "user" | "system";
+        version: string;
         installPath: string;
         installedAt: string;
         lastUpdated: string;
         isLocal: boolean;
         gitCommitSha?: string | undefined;
     }, {
-        version: string;
         scope: "user" | "system";
+        version: string;
         installPath: string;
         installedAt: string;
         lastUpdated: string;
@@ -65,8 +65,8 @@ export declare const InstalledPluginsRegistrySchema: z.ZodObject<{
 }, "strict", z.ZodTypeAny, {
     version: 2;
     plugins: Record<string, {
-        version: string;
         scope: "user" | "system";
+        version: string;
         installPath: string;
         installedAt: string;
         lastUpdated: string;
@@ -76,8 +76,8 @@ export declare const InstalledPluginsRegistrySchema: z.ZodObject<{
 }, {
     version: 2;
     plugins: Record<string, {
-        version: string;
         scope: "user" | "system";
+        version: string;
         installPath: string;
         installedAt: string;
         lastUpdated: string;

package/dist/skill-packager.d.ts

@@ -14,12 +14,11 @@
  * Uses ResourceRegistry + transformContent() from @vibe-agent-toolkit/resources
  * for link resolution and rewriting (replacing the previous inline regex approach).
  */
+import { type ValidationConfig, type ValidationIssue } from '@vibe-agent-toolkit/agent-schema';
 import { ResourceRegistry } from '@vibe-agent-toolkit/resources';
 import { type GitTracker } from '@vibe-agent-toolkit/utils';
-import type { SkillFileEntry } from './files-config.js';
+import { type SkillFileEntry } from './files-config.js';
 import { type PackagingValidationResult } from './validators/packaging-validator.js';
-import type { ValidationIssue } from './validators/types.js';
-import { type ValidationConfig } from './validators/validation-framework.js';
 /**
  * Resource naming strategy type
  */

package/dist/skill-packager.d.ts.map

@@ -1 +1 @@
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package/dist/skill-packager.js

@@ -17,13 +17,14 @@
 import { existsSync, readdirSync, statSync } from 'node:fs';
 import { copyFile, mkdir, readFile, rm, writeFile } from 'node:fs/promises';
 import { basename, dirname } from 'node:path';
-import { ResourceRegistry, loadConfig, openFrontmatter, resolveLocalHref, rewriteFrontmatterUriReferencesFromSchema, transformContent, parseMarkdown, } from '@vibe-agent-toolkit/resources';
+import { runValidationFramework, } from '@vibe-agent-toolkit/agent-schema';
+import { ResourceRegistry, loadConfig, openFrontmatter, resolveLocalHref, rewriteFrontmatterUriReferencesFromSchema, rewriteHtmlLinks, transformContent, parseMarkdown, } from '@vibe-agent-toolkit/resources';
 import { findProjectRoot, resolveAssetReference, toForwardSlash, safePath, } from '@vibe-agent-toolkit/utils';
 import { getTargetSubdir } from './content-type-routing.js';
+import { applyFilesConfig, computeDeferredPaths } from './files-config.js';
 import { checkBrokenPackagedLinks, checkUnreferencedFiles } from './post-build-checks.js';
 import { validateSkillForPackaging } from './validators/packaging-validator.js';
-import { runValidationFramework } from './validators/validation-framework.js';
-import { walkerExclusionsToIssues } from './validators/walker-to-issues.js';
+import { deferredAssetsToIssues, walkerExclusionsToIssues } from './validators/walker-to-issues.js';
 import { walkLinkGraph } from './walk-link-graph.js';
 const PACKAGE_JSON_FILENAME = 'package.json';
 /** Default template for excluded links when no explicit template is configured — renders just the link text */
@@ -108,17 +109,20 @@ export async function packageSkill(skillPath, options = {}) {
     // Find the skill resource in the registry
     const skillResource = registry.getResource(safePath.resolve(skillPath));
     const skillResourceId = skillResource?.id ?? '';
+    const filesConfig = options.files ?? [];
+    const deferredPaths = computeDeferredPaths(filesConfig, { skillDir: skillRoot, projectRoot });
     const packagerWalkOptions = {
         maxDepth,
         excludeRules: excludeConfig?.rules ?? [],
         projectRoot,
         skillRootPath: safePath.resolve(skillPath),
         excludeNavigationFiles,
+        deferredPaths,
     };
     if (options.gitTracker !== undefined) {
         packagerWalkOptions.gitTracker = options.gitTracker;
     }
-    const { bundledResources, bundledAssets, excludedReferences } = walkLinkGraph(skillResourceId, registry, packagerWalkOptions);
+    const { bundledResources, bundledAssets, excludedReferences, deferredAssets } = walkLinkGraph(skillResourceId, registry, packagerWalkOptions);
     // Register non-markdown bundled assets in the source registry so link rewriting
     // can resolve them (resolvedId must be set on links pointing to YAML, JSON, etc.).
     // For any asset whose ID collides with a paired markdown file (e.g. config.yaml +
@@ -148,7 +152,6 @@ export async function packageSkill(skillPath, options = {}) {
     const namingBasePath = projectRoot;
     const pathMap = buildPathMap(skillPath, bundledFiles, outputPath, resourceNaming, namingBasePath, stripPrefix, target);
     // 8b. Apply files config: copy declared files and adjust path map
-    const filesConfig = options.files ?? [];
     for (const fileEntry of filesConfig) {
         const absoluteSource = safePath.resolve(safePath.join(projectRoot, fileEntry.source));
         const absoluteDest = safePath.join(outputPath, fileEntry.dest);
@@ -175,6 +178,10 @@ export async function packageSkill(skillPath, options = {}) {
     }
     // Add non-markdown bundled files (assets) to output registry so link rewriting resolves them
     addBundledAssetsToOutputRegistry(outputResources, bundledAssets, pathMap, registry, collidedAssets);
+    // Register files: deferred-dest links so the build preserves/rewrites them (mirrors
+    // the collided-asset handling). Stamps resolvedId on dest links and adds a synthetic
+    // output resource so the rewriter renders [text](dest) instead of stripping to ().
+    outputResources.push(...registerDeferredDestLinks(filesConfig, collectResourcesWithLinks(bundledResources, skillResource), skillPath, outputPath, outputResources));
     // Include excluded resources (with source paths) for pattern-based rule matching
     for (const excl of excludedReferences) {
         if (excl.excludeReason === 'directory-target' || excl.excludeReason === 'outside-project') {
@@ -213,9 +220,10 @@ export async function packageSkill(skillPath, options = {}) {
         templateContext: { skill: { name: skillMetadata.name } },
         collectionSchemas,
         projectRoot,
+        warn: (message) => process.stderr.write(`warning: ${message}\n`),
     });
     // 12b. Copy files config entries that were not auto-discovered via link traversal.
-    await copyFilesConfigEntries(filesConfig, bundledFiles, projectRoot, outputPath);
+    await applyFilesConfig({ filesConfig, projectRoot, skillOutputDir: outputPath, bundledFiles });
     // 13. Post-build integrity check: no SKILL.md in subdirectories
     // A SKILL.md is a skill definition marker — it must only exist at the root.
     // If another skill's SKILL.md was bundled as a resource, it creates duplicate
@@ -232,7 +240,10 @@ export async function packageSkill(skillPath, options = {}) {
         ...await checkUnreferencedFiles(outputPath),
         ...await checkBrokenPackagedLinks(outputPath),
     ];
-    const rawLinkIssues = walkerExclusionsToIssues(excludedReferences, projectRoot);
+    const rawLinkIssues = [
+        ...walkerExclusionsToIssues(excludedReferences, projectRoot),
+        ...deferredAssetsToIssues(deferredAssets, projectRoot),
+    ];
     const framework = runValidationFramework([...rawLinkIssues, ...rawPostBuildIssues], options.validation ?? {});
     // 13c. Run full validation suite on built output
     const postBuildValidation = await runPostBuildValidation(outputPath, options.validation);
@@ -471,6 +482,73 @@ function buildSyntheticAssetResource(assetPath, outputFilePath) {
         checksum: '0'.repeat(64),
     };
 }
+/**
+ * Register `files:` deferred-dest links so the build preserves and rewrites them.
+ *
+ * A deferred dest (e.g. `dist/bin/cli.mjs → scripts/cli.mjs`) does not exist at
+ * source-walk time, so it is neither a bundled resource nor a bundled asset: its
+ * link gets no `resolvedId` and the dest is absent from the output registry. The
+ * bundled-link template then renders an empty `relativePath` and strips the href
+ * to `()` — leaving the shipped artifact unreferenced (`PACKAGED_UNREFERENCED_FILE`).
+ *
+ * This mirrors the collided-asset handling: for each `files:` entry we synthesize
+ * a stable id (`synthesizeAssetId(absDestTarget)`), stamp it as `resolvedId` on
+ * any local_file link that resolves to the dest, and return a synthetic output
+ * resource (`buildSyntheticAssetResource`) whose `filePath` is the dest's output
+ * path so the output registry computes `relativePath = entry.dest`.
+ *
+ * Scope: dest links only. A SKILL.md link to a deferred *source* path that is
+ * copied to a different dest is an exotic case with ambiguous output mapping and
+ * is intentionally left to its existing behavior.
+ *
+ * @returns Synthetic output resources to push into `outputResources` (deduped by
+ *   filePath against the existing set) BEFORE the output registry is built.
+ */
+function registerDeferredDestLinks(filesConfig, resources, skillPath, outputPath, existingOutputResources) {
+    const syntheticResources = [];
+    const skillDir = dirname(skillPath);
+    for (const entry of filesConfig) {
+        // Where a SKILL.md link `entry.dest` resolves at source time (SKILL.md lives at skillPath).
+        const absDestTarget = safePath.resolve(skillDir, entry.dest);
+        const absDestOutput = safePath.join(outputPath, entry.dest);
+        const id = synthesizeAssetId(absDestTarget);
+        if (!stampDeferredDestResolvedId(resources, absDestTarget, id))
+            continue;
+        // Dedup: skip if an output resource already targets this dest output path.
+        const alreadyPresent = existingOutputResources.some(r => toForwardSlash(r.filePath) === toForwardSlash(absDestOutput)) ||
+            syntheticResources.some(r => toForwardSlash(r.filePath) === toForwardSlash(absDestOutput));
+        if (alreadyPresent)
+            continue;
+        // buildSyntheticAssetResource derives the id via synthesizeAssetId(absDestTarget),
+        // matching the resolvedId stamped above.
+        syntheticResources.push(buildSyntheticAssetResource(absDestTarget, absDestOutput));
+    }
+    return syntheticResources;
+}
+/**
+ * Stamp `resolvedId` on every unresolved local_file link that resolves to the
+ * deferred dest target. Mirrors the link-walk in `resolveCollidedAssetLinks`.
+ *
+ * @returns true if at least one link was stamped (the dest is referenced).
+ */
+function stampDeferredDestResolvedId(resources, absDestTarget, id) {
+    let linked = false;
+    for (const resource of resources) {
+        for (const link of resource.links) {
+            if (link.type !== 'local_file' || link.resolvedId !== undefined) {
+                continue;
+            }
+            const [hrefPath] = link.href.split('#');
+            if (hrefPath === undefined)
+                continue;
+            if (safePath.resolve(dirname(resource.filePath), hrefPath) === absDestTarget) {
+                link.resolvedId = id;
+                linked = true;
+            }
+        }
+    }
+    return linked;
+}
 // ============================================================================
 // Path Map Building
 // ============================================================================
@@ -560,25 +638,6 @@ function buildRewriteRules(excludedIds, excludeRules, defaultExcludeTemplate) {
     }
     return rules;
 }
-/**
- * Copy files config entries that were not auto-discovered via link traversal.
- *
- * Build artifacts declared in `files` (e.g. `dist/bin/cli.mjs → scripts/cli.mjs`)
- * are not in the link graph (the linked path points to `dest`, which doesn't exist
- * at source time). This step copies them explicitly to the output directory.
- */
-async function copyFilesConfigEntries(filesConfig, bundledFiles, projectRoot, outputPath) {
-    const bundledFileSet = new Set(bundledFiles.map(f => toForwardSlash(f)));
-    for (const fileEntry of filesConfig) {
-        const absoluteSource = safePath.resolve(safePath.join(projectRoot, fileEntry.source));
-        const absoluteDest = safePath.join(outputPath, fileEntry.dest);
-        if (!bundledFileSet.has(toForwardSlash(absoluteSource))) {
-            // eslint-disable-next-line security/detect-non-literal-fs-filename -- source path from validated config
-            await mkdir(dirname(absoluteDest), { recursive: true });
-            await copyFile(absoluteSource, absoluteDest);
-        }
-    }
-}
 /**
  * Copy SKILL.md and all linked files to the output directory,
  * rewriting links using transformContent().
@@ -616,8 +675,11 @@ async function copyAndRewriteFile(sourcePath, targetPath, ctx) {
     // Ensure target directory exists
     // eslint-disable-next-line security/detect-non-literal-fs-filename -- targetPath is constructed from validated paths
     await mkdir(dirname(targetPath), { recursive: true });
-    // Non-markdown files or rewriting disabled: plain binary copy
-    if (!sourcePath.endsWith('.md') || !ctx.rewriteLinks) {
+    const lower = sourcePath.toLowerCase();
+    const isMarkdown = lower.endsWith('.md');
+    const isHtml = lower.endsWith('.html') || lower.endsWith('.htm');
+    // Non-rewritable files or rewriting disabled: plain binary copy
+    if ((!isMarkdown && !isHtml) || !ctx.rewriteLinks) {
         await copyFile(sourcePath, targetPath);
         return;
     }
@@ -627,11 +689,27 @@ async function copyAndRewriteFile(sourcePath, targetPath, ctx) {
     // Look up the resource in the "from" registry
     const resource = ctx.fromRegistry.getResource(safePath.resolve(sourcePath));
     if (!resource) {
-        // Resource not in registry — write content as-is
+        // Resource not in registry — write content as-is. For HTML this is only
+        // reachable on an ID collision (e.g. page.html + page.md), where the asset
+        // is copied verbatim and its links are NOT rewritten (v1 limitation,
+        // mirrors the pre-existing asset-collision behavior).
+        ctx.warn(`Copied '${sourcePath}' verbatim without link rewriting: it is not in the resource registry ` +
+            `(typically an ID collision with a same-named markdown file). Source-relative links inside it are not rewritten.`);
         // eslint-disable-next-line security/detect-non-literal-fs-filename -- targetPath is constructed from validated paths
         await writeFile(targetPath, content, 'utf-8');
         return;
     }
+    // HTML: offset-splice link rewrite (no frontmatter, no template body rewrite).
+    if (isHtml) {
+        const rewriteHref = buildHrefRewriter(ctx.fromRegistry, ctx.toRegistry, sourcePath, targetPath, ctx.projectRoot);
+        const rewritten = rewriteHtmlLinks(content, rewriteHref, (info) => {
+            ctx.warn(`Could not rewrite <${info.tagName} ${info.attr}="${info.from}"> in '${sourcePath}' (${info.reason}); ` +
+                `the original value was kept.`);
+        });
+        // eslint-disable-next-line security/detect-non-literal-fs-filename -- targetPath is constructed from validated paths
+        await writeFile(targetPath, rewritten, 'utf-8');
+        return;
+    }
     // Parse once via FrontmatterEditor so comments survive any frontmatter
     // rewrites. The body is held verbatim; we run it through transformContent
     // for the existing rule/template body-link rewrite contract (unchanged).
@@ -649,7 +727,7 @@ async function copyAndRewriteFile(sourcePath, targetPath, ctx) {
     // and body agree on target paths.
     const matchingCollections = (resource.collections ?? []).filter((id) => ctx.collectionSchemas.has(id));
     if (matchingCollections.length > 0) {
-        const rewriteHref = buildFrontmatterHrefRewriter(ctx.fromRegistry, ctx.toRegistry, sourcePath, targetPath, ctx.projectRoot);
+        const rewriteHref = buildHrefRewriter(ctx.fromRegistry, ctx.toRegistry, sourcePath, targetPath, ctx.projectRoot);
         for (const collectionId of matchingCollections) {
             const schema = ctx.collectionSchemas.get(collectionId);
             if (schema) {
@@ -661,7 +739,7 @@ async function copyAndRewriteFile(sourcePath, targetPath, ctx) {
     await writeFile(targetPath, editor.toString(), 'utf-8');
 }
 /**
- * Build the per-href rewrite callback used for frontmatter URI-refs.
+ * Build the per-href rewrite callback used for frontmatter URI-refs and HTML attributes.
  *
  * Mirrors the body-rewrite path so frontmatter and body link rewriting agree
  * on target paths:
@@ -676,7 +754,7 @@ async function copyAndRewriteFile(sourcePath, targetPath, ctx) {
  *
  * Returns the original href when no rewrite applies.
  */
-function buildFrontmatterHrefRewriter(fromRegistry, toRegistry, sourcePath, targetPath, projectRoot) {
+function buildHrefRewriter(fromRegistry, toRegistry, sourcePath, targetPath, projectRoot) {
     const targetDir = dirname(targetPath);
     return (href) => {
         const resolution = resolveLocalHref(href, sourcePath, projectRoot);