@commentray/core 0.1.1 → 0.2.0

package/dist/commentray-disk-pairs.d.ts

@@ -2,6 +2,12 @@ export type DiskCommentrayPair = {
     sourcePath: string;
     commentrayPath: string;
 };
+/**
+ * True when `sourcePath` resolves to a regular file under `repoRoot`.
+ * Used so nav / browse never advertise pairs whose companion exists but the primary source is missing
+ * (otherwise static browse emits URLs with no backing HTML).
+ */
+export declare function commentrayPairSourceFileExistsOnDisk(repoRoot: string, sourcePath: string): Promise<boolean>;
 /**
  * Maps a Markdown path relative to `{storage}/source/` to `(sourcePath, commentrayPath)` using
  * the same flat vs Angles rules as the rest of Commentray.

package/dist/commentray-disk-pairs.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"commentray-disk-pairs.d.ts","sourceRoot":"","sources":["../src/commentray-disk-pairs.ts"],"names":[],"mappings":"AAKA,MAAM,MAAM,kBAAkB,GAAG;IAC/B,UAAU,EAAE,MAAM,CAAC;IACnB,cAAc,EAAE,MAAM,CAAC;CACxB,CAAC;AAEF;;;GAGG;AACH,wBAAgB,2BAA2B,CACzC,cAAc,EAAE,MAAM,EACtB,gBAAgB,EAAE,MAAM,EACxB,QAAQ,EAAE,OAAO,GAChB,kBAAkB,GAAG,IAAI,CAe3B;AAED;;GAEG;AACH,wBAAsB,6BAA6B,CACjD,QAAQ,EAAE,MAAM,EAChB,UAAU,SAAgB,GACzB,OAAO,CAAC,kBAAkB,EAAE,CAAC,CAoB/B"}
+{"version":3,"file":"commentray-disk-pairs.d.ts","sourceRoot":"","sources":["../src/commentray-disk-pairs.ts"],"names":[],"mappings":"AAUA,MAAM,MAAM,kBAAkB,GAAG;IAC/B,UAAU,EAAE,MAAM,CAAC;IACnB,cAAc,EAAE,MAAM,CAAC;CACxB,CAAC;AAEF;;;;GAIG;AACH,wBAAsB,oCAAoC,CACxD,QAAQ,EAAE,MAAM,EAChB,UAAU,EAAE,MAAM,GACjB,OAAO,CAAC,OAAO,CAAC,CASlB;AAED;;;GAGG;AACH,wBAAgB,2BAA2B,CACzC,cAAc,EAAE,MAAM,EACtB,gBAAgB,EAAE,MAAM,EACxB,QAAQ,EAAE,OAAO,GAChB,kBAAkB,GAAG,IAAI,CAe3B;AAED;;GAEG;AACH,wBAAsB,6BAA6B,CACjD,QAAQ,EAAE,MAAM,EAChB,UAAU,SAAgB,GACzB,OAAO,CAAC,kBAAkB,EAAE,CAAC,CAqB/B"}

package/dist/commentray-disk-pairs.js

@@ -1,6 +1,24 @@
+import { stat } from "node:fs/promises";
 import path from "node:path";
-import { commentrayAnglesLayoutEnabled, normalizeRepoRelativePath } from "./paths.js";
+import { commentrayAnglesLayoutEnabled, normalizeRepoRelativePath, resolvePathUnderRepoRoot, } from "./paths.js";
 import { collectMdRelPathsUnderSourceAbs } from "./walk-commentray-source-md.js";
+/**
+ * True when `sourcePath` resolves to a regular file under `repoRoot`.
+ * Used so nav / browse never advertise pairs whose companion exists but the primary source is missing
+ * (otherwise static browse emits URLs with no backing HTML).
+ */
+export async function commentrayPairSourceFileExistsOnDisk(repoRoot, sourcePath) {
+    const rel = sourcePath.trim();
+    if (rel.length === 0)
+        return false;
+    try {
+        const st = await stat(resolvePathUnderRepoRoot(repoRoot, rel));
+        return st.isFile();
+    }
+    catch {
+        return false;
+    }
+}
 /**
  * Maps a Markdown path relative to `{storage}/source/` to `(sourcePath, commentrayPath)` using
  * the same flat vs Angles rules as the rest of Commentray.
@@ -42,6 +60,8 @@ export async function discoverCommentrayPairsOnDisk(repoRoot, storageDir = ".com
         const pair = pairFromCommentraySourceRel(storageNorm, rel, anglesOn);
         if (!pair || seen.has(pair.commentrayPath))
             continue;
+        if (!(await commentrayPairSourceFileExistsOnDisk(repoRoot, pair.sourcePath)))
+            continue;
         seen.add(pair.commentrayPath);
         out.push(pair);
     }

package/dist/commentray-disk-pairs.js.map

@@ -1 +1 @@
-{"version":3,"file":"commentray-disk-pairs.js","sourceRoot":"","sources":["../src/commentray-disk-pairs.ts"],"names":[],"mappings":"AAAA,OAAO,IAAI,MAAM,WAAW,CAAC;AAE7B,OAAO,EAAE,6BAA6B,EAAE,yBAAyB,EAAE,MAAM,YAAY,CAAC;AACtF,OAAO,EAAE,+BAA+B,EAAE,MAAM,gCAAgC,CAAC;AAOjF;;;GAGG;AACH,MAAM,UAAU,2BAA2B,CACzC,cAAsB,EACtB,gBAAwB,EACxB,QAAiB;IAEjB,MAAM,IAAI,GAAG,gBAAgB,CAAC,UAAU,CAAC,IAAI,EAAE,GAAG,CAAC,CAAC;IACpD,IAAI,CAAC,IAAI,CAAC,QAAQ,CAAC,KAAK,CAAC,IAAI,IAAI,KAAK,UAAU,IAAI,IAAI,CAAC,UAAU,CAAC,WAAW,CAAC;QAAE,OAAO,IAAI,CAAC;IAC9F,MAAM,MAAM,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,cAAc,EAAE,QAAQ,EAAE,IAAI,CAAC,CAAC;IAC/D,IAAI,CAAC,QAAQ,EAAE,CAAC;QACd,OAAO,EAAE,UAAU,EAAE,IAAI,CAAC,KAAK,CAAC,CAAC,EAAE,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,IAAI,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,EAAE,cAAc,EAAE,MAAM,EAAE,CAAC;IAC7F,CAAC;IACD,MAAM,GAAG,GAAG,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,CAAC;IACrC,MAAM,IAAI,GAAG,IAAI,CAAC,KAAK,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAC;IACvC,MAAM,IAAI,GAAG,IAAI,CAAC,KAAK,CAAC,CAAC,EAAE,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,IAAI,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC;IACzD,MAAM,cAAc,GAAG,uBAAuB,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;IAC1D,IAAI,GAAG,KAAK,GAAG,IAAI,GAAG,KAAK,EAAE,IAAI,cAAc,EAAE,CAAC;QAChD,OAAO,EAAE,UAAU,EAAE,GAAG,EAAE,cAAc,EAAE,MAAM,EAAE,CAAC;IACrD,CAAC;IACD,OAAO,EAAE,UAAU,EAAE,IAAI,CAAC,KAAK,CAAC,CAAC,EAAE,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,IAAI,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,EAAE,cAAc,EAAE,MAAM,EAAE,CAAC;AAC7F,CAAC;AAED;;GAEG;AACH,MAAM,CAAC,KAAK,UAAU,6BAA6B,CACjD,QAAgB,EAChB,UAAU,GAAG,aAAa;IAE1B,MAAM,WAAW,GAAG,yBAAyB,CAAC,UAAU,CAAC,UAAU,CAAC,IAAI,EAAE,GAAG,CAAC,CAAC,CAAC;IAChF,MAAM,SAAS,GAAG,IAAI,CAAC,IAAI,CAAC,QAAQ,EAAE,GAAG,WAAW,CAAC,KAAK,CAAC,GAAG,CAAC,EAAE,QAAQ,CAAC,CAAC;IAC3E,MAAM,QAAQ,GAAG,6BAA6B,CAAC,QAAQ,EAAE,UAAU,CAAC,CAAC;IACrE,IAAI,IAAc,CAAC;IACnB,IAAI,CAAC;QACH,IAAI,GAAG,MAAM,+BAA+B,CAAC,SAAS,CAAC,CAAC;IAC1D,CAAC;IAAC,MAAM,CAAC;QACP,OAAO,EAAE,CAAC;IACZ,CAAC;IACD,MAAM,GAAG,GAAyB,EAAE,CAAC;IACrC,MAAM,IAAI,GAAG,IAAI,GAAG,EAAU,CAAC;IAC/B,KAAK,MAAM,GAAG,IAAI,IAAI,EAAE,CAAC;QACvB,MAAM,IAAI,GAAG,2BAA2B,CAAC,WAAW,EAAE,GAAG,EAAE,QAAQ,CAAC,CAAC;QACrE,IAAI,CAAC,IAAI,IAAI,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,cAAc,CAAC;YAAE,SAAS;QACrD,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,cAAc,CAAC,CAAC;QAC9B,GAAG,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;IACjB,CAAC;IACD,GAAG,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,cAAc,CAAC,aAAa,CAAC,CAAC,CAAC,cAAc,CAAC,CAAC,CAAC;IACrE,OAAO,GAAG,CAAC;AACb,CAAC"}
+{"version":3,"file":"commentray-disk-pairs.js","sourceRoot":"","sources":["../src/commentray-disk-pairs.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,IAAI,EAAE,MAAM,kBAAkB,CAAC;AACxC,OAAO,IAAI,MAAM,WAAW,CAAC;AAE7B,OAAO,EACL,6BAA6B,EAC7B,yBAAyB,EACzB,wBAAwB,GACzB,MAAM,YAAY,CAAC;AACpB,OAAO,EAAE,+BAA+B,EAAE,MAAM,gCAAgC,CAAC;AAOjF;;;;GAIG;AACH,MAAM,CAAC,KAAK,UAAU,oCAAoC,CACxD,QAAgB,EAChB,UAAkB;IAElB,MAAM,GAAG,GAAG,UAAU,CAAC,IAAI,EAAE,CAAC;IAC9B,IAAI,GAAG,CAAC,MAAM,KAAK,CAAC;QAAE,OAAO,KAAK,CAAC;IACnC,IAAI,CAAC;QACH,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,wBAAwB,CAAC,QAAQ,EAAE,GAAG,CAAC,CAAC,CAAC;QAC/D,OAAO,EAAE,CAAC,MAAM,EAAE,CAAC;IACrB,CAAC;IAAC,MAAM,CAAC;QACP,OAAO,KAAK,CAAC;IACf,CAAC;AACH,CAAC;AAED;;;GAGG;AACH,MAAM,UAAU,2BAA2B,CACzC,cAAsB,EACtB,gBAAwB,EACxB,QAAiB;IAEjB,MAAM,IAAI,GAAG,gBAAgB,CAAC,UAAU,CAAC,IAAI,EAAE,GAAG,CAAC,CAAC;IACpD,IAAI,CAAC,IAAI,CAAC,QAAQ,CAAC,KAAK,CAAC,IAAI,IAAI,KAAK,UAAU,IAAI,IAAI,CAAC,UAAU,CAAC,WAAW,CAAC;QAAE,OAAO,IAAI,CAAC;IAC9F,MAAM,MAAM,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,cAAc,EAAE,QAAQ,EAAE,IAAI,CAAC,CAAC;IAC/D,IAAI,CAAC,QAAQ,EAAE,CAAC;QACd,OAAO,EAAE,UAAU,EAAE,IAAI,CAAC,KAAK,CAAC,CAAC,EAAE,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,IAAI,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,EAAE,cAAc,EAAE,MAAM,EAAE,CAAC;IAC7F,CAAC;IACD,MAAM,GAAG,GAAG,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,CAAC;IACrC,MAAM,IAAI,GAAG,IAAI,CAAC,KAAK,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAC;IACvC,MAAM,IAAI,GAAG,IAAI,CAAC,KAAK,CAAC,CAAC,EAAE,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,IAAI,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC;IACzD,MAAM,cAAc,GAAG,uBAAuB,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;IAC1D,IAAI,GAAG,KAAK,GAAG,IAAI,GAAG,KAAK,EAAE,IAAI,cAAc,EAAE,CAAC;QAChD,OAAO,EAAE,UAAU,EAAE,GAAG,EAAE,cAAc,EAAE,MAAM,EAAE,CAAC;IACrD,CAAC;IACD,OAAO,EAAE,UAAU,EAAE,IAAI,CAAC,KAAK,CAAC,CAAC,EAAE,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,IAAI,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,EAAE,cAAc,EAAE,MAAM,EAAE,CAAC;AAC7F,CAAC;AAED;;GAEG;AACH,MAAM,CAAC,KAAK,UAAU,6BAA6B,CACjD,QAAgB,EAChB,UAAU,GAAG,aAAa;IAE1B,MAAM,WAAW,GAAG,yBAAyB,CAAC,UAAU,CAAC,UAAU,CAAC,IAAI,EAAE,GAAG,CAAC,CAAC,CAAC;IAChF,MAAM,SAAS,GAAG,IAAI,CAAC,IAAI,CAAC,QAAQ,EAAE,GAAG,WAAW,CAAC,KAAK,CAAC,GAAG,CAAC,EAAE,QAAQ,CAAC,CAAC;IAC3E,MAAM,QAAQ,GAAG,6BAA6B,CAAC,QAAQ,EAAE,UAAU,CAAC,CAAC;IACrE,IAAI,IAAc,CAAC;IACnB,IAAI,CAAC;QACH,IAAI,GAAG,MAAM,+BAA+B,CAAC,SAAS,CAAC,CAAC;IAC1D,CAAC;IAAC,MAAM,CAAC;QACP,OAAO,EAAE,CAAC;IACZ,CAAC;IACD,MAAM,GAAG,GAAyB,EAAE,CAAC;IACrC,MAAM,IAAI,GAAG,IAAI,GAAG,EAAU,CAAC;IAC/B,KAAK,MAAM,GAAG,IAAI,IAAI,EAAE,CAAC;QACvB,MAAM,IAAI,GAAG,2BAA2B,CAAC,WAAW,EAAE,GAAG,EAAE,QAAQ,CAAC,CAAC;QACrE,IAAI,CAAC,IAAI,IAAI,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,cAAc,CAAC;YAAE,SAAS;QACrD,IAAI,CAAC,CAAC,MAAM,oCAAoC,CAAC,QAAQ,EAAE,IAAI,CAAC,UAAU,CAAC,CAAC;YAAE,SAAS;QACvF,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,cAAc,CAAC,CAAC;QAC9B,GAAG,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;IACjB,CAAC;IACD,GAAG,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,cAAc,CAAC,aAAa,CAAC,CAAC,CAAC,cAAc,CAAC,CAAC,CAAC;IACrE,OAAO,GAAG,CAAC;AACb,CAAC"}

package/dist/index.d.ts

@@ -9,8 +9,10 @@ export { defaultAngleIdForOpen, FALLBACK_DEFAULT_ANGLE_ID, resolveCommentrayMark
 export type { ResolvedCommentrayMarkdownPath } from "./commentray-path-resolution.js";
 export { commentrayAnglesLayoutEnabled, commentrayAnglesSentinelPath, commentrayMarkdownPath, commentrayMarkdownPathForAngle, defaultMetadataIndexPath, normalizeRepoRelativePath, resolvePathUnderRepoRoot, } from "./paths.js";
 export { findMonorepoPackagesDir, monorepoLayoutStartDir } from "./monorepo-layout.js";
-export { discoverCommentrayPairsOnDisk, pairFromCommentraySourceRel, } from "./commentray-disk-pairs.js";
+export { commentrayPairSourceFileExistsOnDisk, discoverCommentrayPairsOnDisk, pairFromCommentraySourceRel, } from "./commentray-disk-pairs.js";
 export type { DiskCommentrayPair } from "./commentray-disk-pairs.js";
+export { collectOrphanCompanionMarkdownTargets, orphanCompanionCleanupAbsPath, pruneOrphanCompanionMarkdown, } from "./orphan-companion-markdown.js";
+export type { OrphanCompanionMarkdownTarget, PruneOrphanCompanionMarkdownResult, } from "./orphan-companion-markdown.js";
 export type { CommentrayToml, ResolvedAngleDefinition, ResolvedAngles, ResolvedCommentrayConfig, ResolvedGithubNavLink, ResolvedStaticSite, } from "./config.js";
 export { loadCommentrayConfig, mergeCommentrayConfig } from "./config.js";
 export { githubRepoBlobFileUrl, parseGithubRepoWebUrl } from "./github-url.js";
@@ -43,5 +45,5 @@ export type { CommentrayMarkerPair } from "./region-marker-convert.js";
 export { convertCommentraySourceMarkersToLanguage, findCommentrayMarkerPairs, leadingIndentOfLine, } from "./region-marker-convert.js";
 export { MARKER_ID_BODY, assertValidMarkerId, normaliseMarkerSlugOrThrow } from "./marker-ids.js";
 export type { MarkerValidationIssue } from "./marker-validation.js";
-export { validateIndexMarkerSemantics, validateMarkerBoundariesInSource, validateMarkerRegionsAgainstIndexedSources, } from "./marker-validation.js";
+export { extractCommentrayBlockIdsFromMarkdown, validateIndexMarkerSemantics, validateMarkerBoundariesInSource, validateMarkerRegionsAgainstIndexedSources, validateOverlappingMarkerInnerRangesInSource, } from "./marker-validation.js";
 //# sourceMappingURL=index.d.ts.map

package/dist/index.d.ts.map

@@ -1 +1 @@
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package/dist/index.js

@@ -5,7 +5,8 @@ export { applyAnglesFlatMigrationToCommentrayToml, ensureAnglesSentinelFile, ups
 export { defaultAngleIdForOpen, FALLBACK_DEFAULT_ANGLE_ID, resolveCommentrayMarkdownPath, } from "./commentray-path-resolution.js";
 export { commentrayAnglesLayoutEnabled, commentrayAnglesSentinelPath, commentrayMarkdownPath, commentrayMarkdownPathForAngle, defaultMetadataIndexPath, normalizeRepoRelativePath, resolvePathUnderRepoRoot, } from "./paths.js";
 export { findMonorepoPackagesDir, monorepoLayoutStartDir } from "./monorepo-layout.js";
-export { discoverCommentrayPairsOnDisk, pairFromCommentraySourceRel, } from "./commentray-disk-pairs.js";
+export { commentrayPairSourceFileExistsOnDisk, discoverCommentrayPairsOnDisk, pairFromCommentraySourceRel, } from "./commentray-disk-pairs.js";
+export { collectOrphanCompanionMarkdownTargets, orphanCompanionCleanupAbsPath, pruneOrphanCompanionMarkdown, } from "./orphan-companion-markdown.js";
 export { loadCommentrayConfig, mergeCommentrayConfig } from "./config.js";
 export { githubRepoBlobFileUrl, parseGithubRepoWebUrl } from "./github-url.js";
 export { assertValidIndex, emptyIndex } from "./metadata.js";
@@ -25,5 +26,5 @@ export { commentrayRegionInsertions, lineCommentLeaderForLanguage, markerViewpor
 export { CallbackRegionMarkerNamingStrategy, CodeStructureHintStrategy, CompositeRegionMarkerNamingStrategy, defaultRegionMarkerNamingStrategy, EnclosingSymbolHintStrategy, MarkdownHeadingHintStrategy, TomlTableHeaderHintStrategy, tryCodeStructureNameHint, tryMarkdownHeadingTitleAbove, tryNormaliseContextLabelToMarkerId, tryTomlTablePathAboveSelection, } from "./region-marker-naming.js";
 export { convertCommentraySourceMarkersToLanguage, findCommentrayMarkerPairs, leadingIndentOfLine, } from "./region-marker-convert.js";
 export { MARKER_ID_BODY, assertValidMarkerId, normaliseMarkerSlugOrThrow } from "./marker-ids.js";
-export { validateIndexMarkerSemantics, validateMarkerBoundariesInSource, validateMarkerRegionsAgainstIndexedSources, } from "./marker-validation.js";
+export { extractCommentrayBlockIdsFromMarkdown, validateIndexMarkerSemantics, validateMarkerBoundariesInSource, validateMarkerRegionsAgainstIndexedSources, validateOverlappingMarkerInnerRangesInSource, } from "./marker-validation.js";
 //# sourceMappingURL=index.js.map

package/dist/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,wBAAwB,EAAE,sBAAsB,EAAE,MAAM,YAAY,CAAC;AAS9E,OAAO,EACL,eAAe,EACf,uBAAuB,EACvB,mBAAmB,EACnB,eAAe,EACf,wCAAwC,GACzC,MAAM,aAAa,CAAC;AACrB,OAAO,EAAE,kBAAkB,EAAE,MAAM,aAAa,CAAC;AACjD,OAAO,EACL,wCAAwC,EACxC,wBAAwB,EACxB,qCAAqC,GACtC,MAAM,kBAAkB,CAAC;AAK1B,OAAO,EACL,qBAAqB,EACrB,yBAAyB,EACzB,6BAA6B,GAC9B,MAAM,iCAAiC,CAAC;AAEzC,OAAO,EACL,6BAA6B,EAC7B,4BAA4B,EAC5B,sBAAsB,EACtB,8BAA8B,EAC9B,wBAAwB,EACxB,yBAAyB,EACzB,wBAAwB,GACzB,MAAM,YAAY,CAAC;AACpB,OAAO,EAAE,uBAAuB,EAAE,sBAAsB,EAAE,MAAM,sBAAsB,CAAC;AACvF,OAAO,EACL,oCAAoC,EACpC,6BAA6B,EAC7B,2BAA2B,GAC5B,MAAM,4BAA4B,CAAC;AAEpC,OAAO,EACL,qCAAqC,EACrC,6BAA6B,EAC7B,4BAA4B,GAC7B,MAAM,gCAAgC,CAAC;AAaxC,OAAO,EAAE,oBAAoB,EAAE,qBAAqB,EAAE,MAAM,aAAa,CAAC;AAC1E,OAAO,EAAE,qBAAqB,EAAE,qBAAqB,EAAE,MAAM,iBAAiB,CAAC;AAC/E,OAAO,EAAE,gBAAgB,EAAE,UAAU,EAAE,MAAM,eAAe,CAAC;AAC7D,OAAO,EAAE,8BAA8B,EAAE,MAAM,4BAA4B,CAAC;AAC5E,OAAO,EAAE,YAAY,EAAE,MAAM,cAAc,CAAC;AAC5C,OAAO,EACL,kCAAkC,EAClC,mBAAmB,EACnB,iCAAiC,EACjC,kCAAkC,GACnC,MAAM,4BAA4B,CAAC;AAOpC,OAAO,EAAE,eAAe,EAAE,WAAW,EAAE,MAAM,cAAc,CAAC;AAE5D,OAAO,EAAE,cAAc,EAAE,mBAAmB,EAAE,MAAM,2BAA2B,CAAC;AAChF,OAAO,EACL,iCAAiC,EACjC,8BAA8B,GAC/B,MAAM,+BAA+B,CAAC;AAGvC,OAAO,EAAE,aAAa,EAAE,MAAM,gBAAgB,CAAC;AAM/C,OAAO,EACL,SAAS,EACT,4BAA4B,EAC5B,eAAe,EACf,UAAU,GACX,MAAM,uBAAuB,CAAC;AAC/B,OAAO,EAAE,+BAA+B,EAAE,MAAM,4BAA4B,CAAC;AAE7E,OAAO,EAAE,sBAAsB,EAAE,MAAM,uBAAuB,CAAC;AAE/D,OAAO,EAAE,gBAAgB,EAAE,MAAM,oBAAoB,CAAC;AAEtD,OAAO,EACL,qBAAqB,EACrB,iCAAiC,EACjC,kCAAkC,GACnC,MAAM,kBAAkB,CAAC;AAC1B,OAAO,EACL,0BAA0B,EAC1B,4BAA4B,EAC5B,4BAA4B,EAC5B,6BAA6B,EAC7B,0BAA0B,GAC3B,MAAM,qBAAqB,CAAC;AAO7B,OAAO,EACL,kCAAkC,EAClC,yBAAyB,EACzB,mCAAmC,EACnC,iCAAiC,EACjC,2BAA2B,EAC3B,2BAA2B,EAC3B,2BAA2B,EAC3B,wBAAwB,EACxB,4BAA4B,EAC5B,kCAAkC,EAClC,8BAA8B,GAC/B,MAAM,2BAA2B,CAAC;AAEnC,OAAO,EACL,wCAAwC,EACxC,yBAAyB,EACzB,mBAAmB,GACpB,MAAM,4BAA4B,CAAC;AACpC,OAAO,EAAE,cAAc,EAAE,mBAAmB,EAAE,0BAA0B,EAAE,MAAM,iBAAiB,CAAC;AAElG,OAAO,EACL,qCAAqC,EACrC,4BAA4B,EAC5B,gCAAgC,EAChC,0CAA0C,EAC1C,4CAA4C,GAC7C,MAAM,wBAAwB,CAAC"}

package/dist/marker-validation.d.ts

@@ -3,6 +3,15 @@ export type MarkerValidationIssue = {
     level: "error" | "warn";
     message: string;
 };
+/**
+ * Block ids declared in companion markdown via `<!-- commentray:block id=… -->` (valid ids only).
+ */
+export declare function extractCommentrayBlockIdsFromMarkdown(markdown: string): Set<string>;
+/**
+ * Detects two or more well-formed marker regions whose **inner** 1-based inclusive line ranges
+ * intersect. Adjacent regions (last inner line N, next inner starts N+1) do not overlap.
+ */
+export declare function validateOverlappingMarkerInnerRangesInSource(sourceText: string, sourcePath: string): MarkerValidationIssue[];
 /**
  * Scans a single source file for Commentray region / marker boundaries and reports:
  * - invalid ids (syntax that matched but fails `assertValidMarkerId` — rare),
@@ -13,10 +22,14 @@ export type MarkerValidationIssue = {
 export declare function validateMarkerBoundariesInSource(sourceText: string, sourcePath: string): MarkerValidationIssue[];
 /**
  * For each `marker:` block, ensures the primary file contains a well-formed paired
- * region that resolves to a non-empty span. Warns when a paired region exists in
- * the primary but no indexed block claims `marker:<id>` (orphan region).
+ * region that resolves to a non-empty span.
+ *
+ * When `markdownBlockIdsBySourceNorm` is set (repo validation), warns for **orphan** regions: a
+ * paired delimiter id in the primary that has no matching `<!-- commentray:block id=… -->` in any
+ * indexed companion markdown for that primary. When it is omitted (tests), the legacy rule
+ * applies: warn only when no indexed block claims `marker:<id>`.
  */
-export declare function validateMarkerRegionsAgainstIndexedSources(index: CommentrayIndex, indexedSourceTexts: Map<string, string>): MarkerValidationIssue[];
+export declare function validateMarkerRegionsAgainstIndexedSources(index: CommentrayIndex, indexedSourceTexts: Map<string, string>, markdownBlockIdsBySourceNorm?: Map<string, Set<string>>): MarkerValidationIssue[];
 /**
  * Index-level rules for stable cross-references:
  * - **Error** if the same `(sourcePath, marker id)` is claimed by **different** block `id`s

package/dist/marker-validation.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"marker-validation.d.ts","sourceRoot":"","sources":["../src/marker-validation.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,eAAe,EAAE,MAAM,YAAY,CAAC;AAKlD,MAAM,MAAM,qBAAqB,GAAG;IAAE,KAAK,EAAE,OAAO,GAAG,MAAM,CAAC;IAAC,OAAO,EAAE,MAAM,CAAA;CAAE,CAAC;AAEjF;;;;;;GAMG;AACH,wBAAgB,gCAAgC,CAC9C,UAAU,EAAE,MAAM,EAClB,UAAU,EAAE,MAAM,GACjB,qBAAqB,EAAE,CAkDzB;AA0FD;;;;GAIG;AACH,wBAAgB,0CAA0C,CACxD,KAAK,EAAE,eAAe,EACtB,kBAAkB,EAAE,GAAG,CAAC,MAAM,EAAE,MAAM,CAAC,GACtC,qBAAqB,EAAE,CAMzB;AAmBD;;;;;;GAMG;AACH,wBAAgB,4BAA4B,CAAC,KAAK,EAAE,eAAe,GAAG,qBAAqB,EAAE,CAuD5F"}
+{"version":3,"file":"marker-validation.d.ts","sourceRoot":"","sources":["../src/marker-validation.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,eAAe,EAAE,MAAM,YAAY,CAAC;AAKlD,MAAM,MAAM,qBAAqB,GAAG;IAAE,KAAK,EAAE,OAAO,GAAG,MAAM,CAAC;IAAC,OAAO,EAAE,MAAM,CAAA;CAAE,CAAC;AAEjF;;GAEG;AACH,wBAAgB,qCAAqC,CAAC,QAAQ,EAAE,MAAM,GAAG,GAAG,CAAC,MAAM,CAAC,CAanF;AAED;;;GAGG;AACH,wBAAgB,4CAA4C,CAC1D,UAAU,EAAE,MAAM,EAClB,UAAU,EAAE,MAAM,GACjB,qBAAqB,EAAE,CA4BzB;AAED;;;;;;GAMG;AACH,wBAAgB,gCAAgC,CAC9C,UAAU,EAAE,MAAM,EAClB,UAAU,EAAE,MAAM,GACjB,qBAAqB,EAAE,CAmDzB;AAgHD;;;;;;;;GAQG;AACH,wBAAgB,0CAA0C,CACxD,KAAK,EAAE,eAAe,EACtB,kBAAkB,EAAE,GAAG,CAAC,MAAM,EAAE,MAAM,CAAC,EACvC,4BAA4B,CAAC,EAAE,GAAG,CAAC,MAAM,EAAE,GAAG,CAAC,MAAM,CAAC,CAAC,GACtD,qBAAqB,EAAE,CAMzB;AAmBD;;;;;;GAMG;AACH,wBAAgB,4BAA4B,CAAC,KAAK,EAAE,eAAe,GAAG,qBAAqB,EAAE,CAuD5F"}

package/dist/marker-validation.js

@@ -1,8 +1,62 @@
 import { parseAnchor } from "./anchors.js";
-import { assertValidMarkerId } from "./marker-ids.js";
+import { assertValidMarkerId, MARKER_ID_BODY } from "./marker-ids.js";
 import { normalizeRepoRelativePath } from "./paths.js";
 import { findCommentrayMarkerPairs } from "./region-marker-convert.js";
 import { parseCommentrayRegionBoundary, sourceLineRangeForMarkerId } from "./source-markers.js";
+/**
+ * Block ids declared in companion markdown via `<!-- commentray:block id=… -->` (valid ids only).
+ */
+export function extractCommentrayBlockIdsFromMarkdown(markdown) {
+    const out = new Set();
+    const re = new RegExp(`<!--\\s*commentray:block\\s+id=(${MARKER_ID_BODY})\\s*-->`, "gi");
+    for (const m of markdown.matchAll(re)) {
+        const raw = m[1];
+        if (raw === undefined)
+            continue;
+        try {
+            out.add(assertValidMarkerId(raw));
+        }
+        catch {
+            /* ignore malformed ids on that line */
+        }
+    }
+    return out;
+}
+/**
+ * Detects two or more well-formed marker regions whose **inner** 1-based inclusive line ranges
+ * intersect. Adjacent regions (last inner line N, next inner starts N+1) do not overlap.
+ */
+export function validateOverlappingMarkerInnerRangesInSource(sourceText, sourcePath) {
+    const text = sourceText.replaceAll("\r\n", "\n");
+    const pairs = findCommentrayMarkerPairs(text);
+    const ranges = [];
+    for (const pair of pairs) {
+        const r = sourceLineRangeForMarkerId(text, pair.id);
+        if (r === null)
+            continue;
+        ranges.push({ id: pair.id, start: r.start, end: r.end });
+    }
+    const issues = [];
+    for (let i = 0; i < ranges.length; i++) {
+        const a = ranges[i];
+        if (a === undefined)
+            continue;
+        for (let j = i + 1; j < ranges.length; j++) {
+            const b = ranges[j];
+            if (b === undefined)
+                continue;
+            if (a.end < b.start || b.end < a.start)
+                continue;
+            issues.push({
+                level: "error",
+                message: `${sourcePath}: commentray regions "${a.id}" (inner lines ${a.start}–${a.end}) and "${b.id}" ` +
+                    `(${b.start}–${b.end}) overlap. Regions in the same primary file must not share source lines — ` +
+                    `close one region before the other begins, or split the file.`,
+            });
+        }
+    }
+    return issues;
+}
 /**
  * Scans a single source file for Commentray region / marker boundaries and reports:
  * - invalid ids (syntax that matched but fails `assertValidMarkerId` — rare),
@@ -58,6 +112,7 @@ export function validateMarkerBoundariesInSource(sourceText, sourcePath) {
             message: `${sourcePath}:${line0 + 1}: commentray start for id "${id}" has no matching end in this file.`,
         });
     }
+    issues.push(...validateOverlappingMarkerInnerRangesInSource(sourceText, sourcePath));
     return issues;
 }
 function tryParseMarkerAnchorId(anchor) {
@@ -113,19 +168,38 @@ function displaySourcePathForNorm(index, norm) {
     const hit = Object.values(index.byCommentrayPath).find((e) => normalizeRepoRelativePath(e.sourcePath) === norm);
     return hit?.sourcePath ?? norm;
 }
-function orphanRegionIssues(index, indexedSourceTexts, claimedBySourceNorm) {
+function orphanRegionIssues(index, indexedSourceTexts, claimedBySourceNorm, markdownBlockIdsBySourceNorm) {
     const issues = [];
     const orphanWarned = new Set();
     for (const [norm, text] of indexedSourceTexts) {
         const pairs = findCommentrayMarkerPairs(text);
         const claimed = claimedBySourceNorm.get(norm) ?? new Set();
+        const mdIds = markdownBlockIdsBySourceNorm?.get(norm);
         const displayPath = displaySourcePathForNorm(index, norm);
         for (const pair of pairs) {
-            if (claimed.has(pair.id))
-                continue;
             const dedupe = `${norm}\0${pair.id}`;
             if (orphanWarned.has(dedupe))
                 continue;
+            if (markdownBlockIdsBySourceNorm !== undefined) {
+                const inMd = mdIds?.has(pair.id) ?? false;
+                if (inMd)
+                    continue;
+                orphanWarned.add(dedupe);
+                const indexed = claimed.has(pair.id);
+                const tail = indexed
+                    ? ` An indexed block uses anchor marker:${pair.id}, but no companion markdown line ` +
+                        `\`<!-- commentray:block id=${pair.id} -->\` was found for this primary (add the marker or fix the path).`
+                    : ` No indexed block uses anchor marker:${pair.id}, and no companion markdown references this id.`;
+                issues.push({
+                    level: "warn",
+                    message: `Primary "${displayPath}" has a commentray region "${pair.id}" (delimiter lines ` +
+                        `${pair.startLine0 + 1} and ${pair.endLine0 + 1}) that is not referenced by any ` +
+                        `\`<!-- commentray:block id=${pair.id} -->\` line in companion markdown for this primary.${tail}`,
+                });
+                continue;
+            }
+            if (claimed.has(pair.id))
+                continue;
             orphanWarned.add(dedupe);
             issues.push({
                 level: "warn",
@@ -140,14 +214,18 @@ function orphanRegionIssues(index, indexedSourceTexts, claimedBySourceNorm) {
 }
 /**
  * For each `marker:` block, ensures the primary file contains a well-formed paired
- * region that resolves to a non-empty span. Warns when a paired region exists in
- * the primary but no indexed block claims `marker:<id>` (orphan region).
+ * region that resolves to a non-empty span.
+ *
+ * When `markdownBlockIdsBySourceNorm` is set (repo validation), warns for **orphan** regions: a
+ * paired delimiter id in the primary that has no matching `<!-- commentray:block id=… -->` in any
+ * indexed companion markdown for that primary. When it is omitted (tests), the legacy rule
+ * applies: warn only when no indexed block claims `marker:<id>`.
  */
-export function validateMarkerRegionsAgainstIndexedSources(index, indexedSourceTexts) {
+export function validateMarkerRegionsAgainstIndexedSources(index, indexedSourceTexts, markdownBlockIdsBySourceNorm) {
     const claimed = claimedMarkerIdsByNormalizedSource(index);
     return [
         ...unresolvedMarkerAnchorIssues(index, indexedSourceTexts),
-        ...orphanRegionIssues(index, indexedSourceTexts, claimed),
+        ...orphanRegionIssues(index, indexedSourceTexts, claimed, markdownBlockIdsBySourceNorm),
     ];
 }
 function markerIdFromBlock(block) {

package/dist/marker-validation.js.map

@@ -1 +1 @@
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package/dist/monorepo-layout.d.ts

@@ -1,7 +1,7 @@
 /**
  * Starting directory for locating the monorepo `packages/` folder: typically
  * `dirname(import.meta.url)` in normal ESM, or `dirname(process.argv[1])` when
- * `import.meta.url` is missing (e.g. code bundled into @commentray/cli's single
+ * `import.meta.url` is missing (e.g. code bundled into the commentray CLI's single
  * CJS file, where esbuild emits empty `import.meta` shims for nested packages).
  */
 export declare function monorepoLayoutStartDir(importMetaUrl: string | undefined): string;

package/dist/monorepo-layout.js

@@ -4,7 +4,7 @@ import { fileURLToPath } from "node:url";
 /**
  * Starting directory for locating the monorepo `packages/` folder: typically
  * `dirname(import.meta.url)` in normal ESM, or `dirname(process.argv[1])` when
- * `import.meta.url` is missing (e.g. code bundled into @commentray/cli's single
+ * `import.meta.url` is missing (e.g. code bundled into the commentray CLI's single
  * CJS file, where esbuild emits empty `import.meta` shims for nested packages).
  */
 export function monorepoLayoutStartDir(importMetaUrl) {

package/dist/orphan-companion-markdown.d.ts

@@ -0,0 +1,32 @@
+export type OrphanCompanionMarkdownTarget = {
+    /** Repo-relative companion path (POSIX, e.g. `.commentray/source/docs/plan/plan.md/main.md`). */
+    commentrayPath: string;
+    /** Inferred primary source path the companion belongs to (missing as a regular file). */
+    sourcePath: string;
+    /** Absolute path to remove: a single `.md` file (flat) or an Angles directory under `source/`. */
+    absCleanupPath: string;
+    /** When true, `pruneOrphanCompanionMarkdown` removes a directory tree; otherwise one file. */
+    cleanupIsDirectory: boolean;
+};
+/**
+ * Absolute path under `{storage}/source/` to remove so this companion no longer appears in discovery.
+ * Flat: the lone `*.md` file. Angles: the per-source directory (parent of `*.md` angle files).
+ */
+export declare function orphanCompanionCleanupAbsPath(repoRoot: string, storageDirNorm: string, relFromSourceDir: string, anglesOn: boolean): string;
+/**
+ * Lists companion Markdown trees/files under `{storage}/source/` whose inferred primary source file
+ * is missing from the repo (same rule as static nav / discover).
+ */
+export declare function collectOrphanCompanionMarkdownTargets(repoRoot: string, storageDir?: string): Promise<OrphanCompanionMarkdownTarget[]>;
+export type PruneOrphanCompanionMarkdownResult = {
+    /** Repo-relative POSIX paths that were removed (files) or directories (shown as trailing `/` optional — use absolute in log). */
+    removedAbsPaths: string[];
+};
+/**
+ * Deletes orphan companion storage discovered by {@link collectOrphanCompanionMarkdownTargets}.
+ * Only removes paths previously identified as orphan cleanup targets (under `{storage}/source/`).
+ */
+export declare function pruneOrphanCompanionMarkdown(repoRoot: string, storageDir?: string, options?: {
+    dryRun?: boolean;
+}): Promise<PruneOrphanCompanionMarkdownResult>;
+//# sourceMappingURL=orphan-companion-markdown.d.ts.map

package/dist/orphan-companion-markdown.d.ts.map

@@ -0,0 +1 @@
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package/dist/orphan-companion-markdown.js

@@ -0,0 +1,91 @@
+import { rm, stat, unlink } from "node:fs/promises";
+import path from "node:path";
+import { commentrayAnglesLayoutEnabled, normalizeRepoRelativePath } from "./paths.js";
+import { commentrayPairSourceFileExistsOnDisk, pairFromCommentraySourceRel, } from "./commentray-disk-pairs.js";
+import { collectMdRelPathsUnderSourceAbs } from "./walk-commentray-source-md.js";
+/**
+ * Absolute path under `{storage}/source/` to remove so this companion no longer appears in discovery.
+ * Flat: the lone `*.md` file. Angles: the per-source directory (parent of `*.md` angle files).
+ */
+export function orphanCompanionCleanupAbsPath(repoRoot, storageDirNorm, relFromSourceDir, anglesOn) {
+    const sourceAbs = path.join(repoRoot, ...storageDirNorm.split("/"), "source");
+    if (!anglesOn) {
+        return path.join(sourceAbs, ...relFromSourceDir.split("/"));
+    }
+    const parent = path.posix.dirname(relFromSourceDir);
+    if (parent === "." || parent === "") {
+        return path.join(sourceAbs, ...relFromSourceDir.split("/"));
+    }
+    return path.join(sourceAbs, ...parent.split("/"));
+}
+/**
+ * Lists companion Markdown trees/files under `{storage}/source/` whose inferred primary source file
+ * is missing from the repo (same rule as static nav / discover).
+ */
+export async function collectOrphanCompanionMarkdownTargets(repoRoot, storageDir = ".commentray") {
+    const storageNorm = normalizeRepoRelativePath(storageDir.replaceAll("\\", "/"));
+    const sourceAbs = path.join(repoRoot, ...storageNorm.split("/"), "source");
+    let rels;
+    try {
+        rels = await collectMdRelPathsUnderSourceAbs(sourceAbs);
+    }
+    catch {
+        return [];
+    }
+    const anglesOn = commentrayAnglesLayoutEnabled(repoRoot, storageDir);
+    const byCleanupAbs = new Map();
+    for (const rel of rels) {
+        const pair = pairFromCommentraySourceRel(storageNorm, rel, anglesOn);
+        if (!pair)
+            continue;
+        if (await commentrayPairSourceFileExistsOnDisk(repoRoot, pair.sourcePath))
+            continue;
+        const absCleanupPath = orphanCompanionCleanupAbsPath(repoRoot, storageNorm, rel, anglesOn);
+        let cleanupIsDirectory;
+        try {
+            const st = await stat(absCleanupPath);
+            cleanupIsDirectory = st.isDirectory();
+        }
+        catch {
+            continue;
+        }
+        const key = absCleanupPath;
+        if (byCleanupAbs.has(key))
+            continue;
+        byCleanupAbs.set(key, {
+            commentrayPath: pair.commentrayPath,
+            sourcePath: pair.sourcePath,
+            absCleanupPath,
+            cleanupIsDirectory,
+        });
+    }
+    return [...byCleanupAbs.values()].sort((a, b) => a.commentrayPath.localeCompare(b.commentrayPath));
+}
+/**
+ * Deletes orphan companion storage discovered by {@link collectOrphanCompanionMarkdownTargets}.
+ * Only removes paths previously identified as orphan cleanup targets (under `{storage}/source/`).
+ */
+export async function pruneOrphanCompanionMarkdown(repoRoot, storageDir = ".commentray", options) {
+    const targets = await collectOrphanCompanionMarkdownTargets(repoRoot, storageDir);
+    const removedAbsPaths = [];
+    const dryRun = options?.dryRun === true;
+    const storageNorm = normalizeRepoRelativePath(storageDir.replaceAll("\\", "/"));
+    const sourceAbs = path.join(repoRoot, ...storageNorm.split("/"), "source");
+    for (const t of targets) {
+        if (!t.absCleanupPath.startsWith(sourceAbs))
+            continue;
+        if (dryRun) {
+            removedAbsPaths.push(t.absCleanupPath);
+            continue;
+        }
+        if (t.cleanupIsDirectory) {
+            await rm(t.absCleanupPath, { recursive: true, maxRetries: 2, retryDelay: 50 });
+        }
+        else {
+            await unlink(t.absCleanupPath);
+        }
+        removedAbsPaths.push(t.absCleanupPath);
+    }
+    return { removedAbsPaths };
+}
+//# sourceMappingURL=orphan-companion-markdown.js.map

package/dist/orphan-companion-markdown.js.map

@@ -0,0 +1 @@
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package/dist/validate-project.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"validate-project.d.ts","sourceRoot":"","sources":["../src/validate-project.ts"],"names":[],"mappings":"AAOA,OAAO,EAAoD,KAAK,eAAe,EAAE,MAAM,YAAY,CAAC;AAapG,MAAM,MAAM,eAAe,GAAG;IAAE,KAAK,EAAE,OAAO,GAAG,MAAM,CAAC;IAAC,OAAO,EAAE,MAAM,CAAA;CAAE,CAAC;AAE3E,MAAM,MAAM,gBAAgB,GAAG;IAC7B,MAAM,EAAE,eAAe,EAAE,CAAC;CAC3B,CAAC;AAEF,MAAM,MAAM,sBAAsB,GAAG;IACnC;;;;OAIG;IACH,uBAAuB,CAAC,EAAE,SAAS,MAAM,EAAE,CAAC;CAC7C,CAAC;AAwLF,wBAAsB,eAAe,CACnC,QAAQ,EAAE,MAAM,EAChB,OAAO,CAAC,EAAE,sBAAsB,GAC/B,OAAO,CAAC,gBAAgB,CAAC,CAuD3B;AAiBD;;;GAGG;AACH,wBAAsB,4BAA4B,CAChD,QAAQ,EAAE,MAAM,GACf,OAAO,CAAC;IAAE,KAAK,EAAE,eAAe,CAAC;IAAC,OAAO,EAAE,OAAO,CAAA;CAAE,CAAC,CAqBvD;AAED,wBAAsB,SAAS,CAAC,QAAQ,EAAE,MAAM,GAAG,OAAO,CAAC,eAAe,GAAG,IAAI,CAAC,CASjF;AAED;;;;GAIG;AACH,wBAAsB,UAAU,CAAC,QAAQ,EAAE,MAAM,EAAE,KAAK,EAAE,eAAe,GAAG,OAAO,CAAC,IAAI,CAAC,CAKxF"}

package/dist/validate-project.js

@@ -7,9 +7,10 @@ import { assertValidIndex } from "./metadata.js";
 import { migrateIndex } from "./migrate.js";
 import { coerceIndexSchemaVersion, CURRENT_SCHEMA_VERSION } from "./model.js";
 import { defaultMetadataIndexPath, normalizeRepoRelativePath } from "./paths.js";
-import { validateIndexMarkerSemantics, validateMarkerBoundariesInSource, validateMarkerRegionsAgainstIndexedSources, } from "./marker-validation.js";
+import { extractCommentrayBlockIdsFromMarkdown, validateIndexMarkerSemantics, validateMarkerBoundariesInSource, validateMarkerRegionsAgainstIndexedSources, } from "./marker-validation.js";
 import { loadGitTrackedSourceTextsOutsideIndex } from "./git-relocation-scan.js";
 import { relocationHintMessages } from "./relocation-hints.js";
+import { collectOrphanCompanionMarkdownTargets } from "./orphan-companion-markdown.js";
 import { GitScmProvider } from "./scm/git-scm-provider.js";
 function stagedPathsSet(paths) {
     return new Set(paths.map((p) => normalizeRepoRelativePath(p)));
@@ -19,6 +20,28 @@ function stagedScopeNeedsFullIndexValidation(staged) {
     const toml = normalizeRepoRelativePath(".commentray.toml");
     return staged.has(indexJson) || staged.has(toml);
 }
+async function loadMarkdownBlockIdsByIndexedSource(repoRoot, index) {
+    const bySource = new Map();
+    for (const [crPath, entry] of Object.entries(index.byCommentrayPath)) {
+        const norm = normalizeRepoRelativePath(entry.sourcePath);
+        let set = bySource.get(norm);
+        if (!set) {
+            set = new Set();
+            bySource.set(norm, set);
+        }
+        const abs = path.join(repoRoot, crPath);
+        try {
+            const md = await fs.readFile(abs, "utf8");
+            for (const id of extractCommentrayBlockIdsFromMarkdown(md)) {
+                set.add(id);
+            }
+        }
+        catch {
+            /* missing or unreadable companion — other validation may warn */
+        }
+    }
+    return bySource;
+}
 function indexFilteredForStaged(index, staged) {
     const next = {};
     for (const [crPath, entry] of Object.entries(index.byCommentrayPath)) {
@@ -65,7 +88,8 @@ async function collectIssuesForLoadedIndex(repoRoot, index) {
             issues.push({ level: issue.level, message: issue.message });
         }
     }
-    for (const issue of validateMarkerRegionsAgainstIndexedSources(index, indexedSourceTexts)) {
+    const markdownBlockIdsBySourceNorm = await loadMarkdownBlockIdsByIndexedSource(repoRoot, index);
+    for (const issue of validateMarkerRegionsAgainstIndexedSources(index, indexedSourceTexts, markdownBlockIdsBySourceNorm)) {
         issues.push({ level: issue.level, message: issue.message });
     }
     if (missingSourcesNorm.size === 0)
@@ -100,6 +124,41 @@ async function collectIssuesForLoadedIndex(repoRoot, index) {
     }
     return issues;
 }
+async function pushMissingStorageSubdirWarnings(repoRoot, storageDir, issues) {
+    const storageAbs = path.join(repoRoot, storageDir);
+    for (const sub of ["source", "metadata"]) {
+        const p = path.join(storageAbs, sub);
+        try {
+            await fs.stat(p);
+        }
+        catch {
+            issues.push({
+                level: "warn",
+                message: `Missing directory: ${path.join(storageDir, sub)}`,
+            });
+        }
+    }
+}
+async function pushOrphanCompanionMarkdownIssues(repoRoot, storageDir, issues) {
+    try {
+        const orphans = await collectOrphanCompanionMarkdownTargets(repoRoot, storageDir);
+        for (const o of orphans) {
+            const relCleanup = normalizeRepoRelativePath(path.relative(repoRoot, o.absCleanupPath).replaceAll("\\", "/"));
+            issues.push({
+                level: "error",
+                message: `Orphan companion Markdown: primary source "${o.sourcePath}" is not a readable file, but ` +
+                    `companion storage exists (${o.commentrayPath}). Static browse and search would advertise a broken pair. ` +
+                    `Delete this orphan with: commentray doctor --allow-deletions (removes ${relCleanup})`,
+            });
+        }
+    }
+    catch (err) {
+        issues.push({
+            level: "warn",
+            message: `Could not scan for orphan companion Markdown: ${err instanceof Error ? err.message : String(err)}`,
+        });
+    }
+}
 export async function validateProject(repoRoot, options) {
     const issues = [];
     let config;
@@ -113,19 +172,8 @@ export async function validateProject(repoRoot, options) {
         });
         return { issues };
     }
-    const storageAbs = path.join(repoRoot, config.storageDir);
-    for (const sub of ["source", "metadata"]) {
-        const p = path.join(storageAbs, sub);
-        try {
-            await fs.stat(p);
-        }
-        catch {
-            issues.push({
-                level: "warn",
-                message: `Missing directory: ${path.join(config.storageDir, sub)}`,
-            });
-        }
-    }
+    await pushMissingStorageSubdirWarnings(repoRoot, config.storageDir, issues);
+    await pushOrphanCompanionMarkdownIssues(repoRoot, config.storageDir, issues);
     let index = null;
     try {
         index = await readIndex(repoRoot);

package/dist/validate-project.js.map

@@ -1 +1 @@
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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@commentray/core",
-  "version": "0.1.1",
+  "version": "0.2.0",
   "publishConfig": {
     "access": "public"
   },