fix: route lint-view + sources-view deletes through the unified ref-cleanup helper

Three delete paths existed in the codebase, with three different
cleanup behaviours, and only the newest one cleaned everything:

  Knowledge tree right-click (new)  body + index + related: ✓
  Sources view source delete cascade body + index, NOT related: ✗
  Lint view orphan delete            nothing                ✗

The user-visible symptom was the FrontmatterPanel rendering an
AlertTriangle next to a `related:` slug that pointed at a page
deleted via Sources view or Lint view — the page was gone, so the
slug couldn't resolve, but no cleanup pass had filtered it out of
its referrer's frontmatter array. After deletion the right thing to
do is remove the dangling reference, not show the user a broken-link
warning that they then have to fix by hand.

Both call sites now go through `cascadeDeleteWikiPagesWithRefs`
which already handles the full sweep (body wikilinks via
stripDeletedWikilinks, index.md listing via cleanIndexListing, and
`related:` filtering via parseFrontmatterArray + writeFrontmatterArray
on every surviving wiki .md). Sources view's previous inline cleanup
loop and the now-orphaned `flattenMdFiles` local helper are removed
along with the unused wiki-cleanup imports.

Tests: 7 cases on the helper itself were added in the previous
commit and cover both the body-wikilink and related-frontmatter
paths plus the substring-collision regression. Existing
sources-view + lint-view flows have no targeted unit tests, but the
full unit suite (984 cases) passes and the helper's tests pin the
behaviour now shared by all three call sites.

Author: nashsu

src/components/lint/lint-view.tsx

@@ -181,10 +181,16 @@ export function LintView() {
     if (!confirmed) return
 
     try {
-      // Cascade = deleteFile(...) + drop the orphan page's embedding
-      // chunks so it stops showing up as a phantom vector hit.
-      const { cascadeDeleteWikiPage } = await import("@/lib/wiki-page-delete")
-      await cascadeDeleteWikiPage(pp, pagePath)
+      // Full cascade: file + embedding chunks + every reference to
+      // the page across the wiki (body wikilinks, index.md listing,
+      // `related:` frontmatter arrays). Even though "orphan" by lint
+      // means no incoming wikilinks were detected, `related:` slugs
+      // and index.md entries can still point at it — the orphan
+      // detector only walks body refs.
+      const { cascadeDeleteWikiPagesWithRefs } = await import(
+        "@/lib/wiki-page-delete"
+      )
+      await cascadeDeleteWikiPagesWithRefs(pp, [pagePath])
       setResults((prev) => prev.filter((_, i) => i !== index))
       const tree = await listDirectory(pp)
       setFileTree(tree)

src/components/sources/sources-view.tsx

@@ -11,13 +11,6 @@ import { enqueueIngest, enqueueBatch } from "@/lib/ingest-queue"
 import { hasUsableLlm } from "@/lib/has-usable-llm"
 import { useTranslation } from "react-i18next"
 import { normalizePath, getFileName } from "@/lib/path-utils"
-import {
-  buildDeletedKeys,
-  cleanIndexListing,
-  stripDeletedWikilinks,
-  extractFrontmatterTitle,
-  type DeletedPageInfo,
-} from "@/lib/wiki-cleanup"
 import { parseSources, writeSources } from "@/lib/sources-merge"
 import { decidePageFate } from "@/lib/source-delete-decision"
 import { removeFromIngestCache } from "@/lib/ingest-cache"
@@ -347,8 +340,11 @@ export function SourcesView() {
       //            elsewhere in the frontmatter). Leaving the page
       //            alone prevents silent data loss when a filename
       //            happens to appear in an unrelated page's metadata.
-      const actuallyDeleted: string[] = []
-      const deletedInfos: DeletedPageInfo[] = []
+      // Pass 1: keep / skip — rewrite sources for shared pages, no
+      // deletion needed. The "delete" decisions are deferred to a
+      // single batch call after the loop so we can route them
+      // through the unified cascade helper.
+      const pagesToDelete: string[] = []
       for (const pagePath of relatedPages) {
         try {
           const content = await readFile(pagePath)
@@ -369,64 +365,28 @@ export function SourcesView() {
             continue
           }
 
-          // action === "delete": the page's sole source was this file.
-          // Capture slug + title before deletion so stale references
-          // can be cleaned from index / overview / sibling pages.
-          const slug = getFileName(pagePath).replace(/\.md$/, "")
-          const title = extractFrontmatterTitle(content)
-          deletedInfos.push({ slug, title })
-          // cascadeDeleteWikiPage = deleteFile(...) + drop the page's
-          // embedding chunks so future searches don't return phantom
-          // hits pointing at a file that no longer exists.
-          const { cascadeDeleteWikiPage } = await import("@/lib/wiki-page-delete")
-          await cascadeDeleteWikiPage(pp, pagePath)
-          actuallyDeleted.push(pagePath)
+          // action === "delete" → defer.
+          pagesToDelete.push(pagePath)
         } catch (err) {
           console.error(`Failed to process wiki page ${pagePath}:`, err)
         }
       }
 
-      // Steps 5 & 6: clean stale references from every wiki file.
-      //
-      // index.md  → drop list-item lines whose primary `[[target]]` is
-      //             a deleted page (title OR slug form matches).
-      // overview.md + everything else → strip `[[deleted]]` occurrences
-      //             in prose, replacing them with plain text (or with
-      //             the pipe display when present).
-      //
-      // Using normalized-key matching rather than the old substring
-      // `includes` check avoids two classes of real bugs: stale
-      // title-form refs surviving (`[[KV Cache]]` vs slug `kv-cache`),
-      // and innocent siblings getting wiped collaterally (deleting
-      // `ai.md` must not take `[[OpenAI]]` / `[[AI Safety]]` down).
-      const deletedKeys = buildDeletedKeys(deletedInfos)
-      if (deletedKeys.size > 0) {
-        try {
-          const wikiTree = await listDirectory(`${pp}/wiki`)
-          const allMdFiles = flattenMdFiles(wikiTree)
-          for (const file of allMdFiles) {
-            try {
-              const content = await readFile(file.path)
-              const isIndex = file.path === `${pp}/wiki/index.md` ||
-                file.name === "index.md"
-              // For index: first drop whole entry lines for deleted
-              // pages, then still strip any secondary `[[...]]` refs
-              // to deleted pages that may appear in surviving rows.
-              const afterListing = isIndex
-                ? cleanIndexListing(content, deletedKeys)
-                : content
-              const updated = stripDeletedWikilinks(afterListing, deletedKeys)
-              if (updated !== content) {
-                await writeFile(file.path, updated)
-              }
-            } catch {
-              // skip individual file failures — best-effort cleanup
-            }
-          }
-        } catch {
-          // non-critical
-        }
-      }
+      // Pass 2: full cascade for every page whose sole source was
+      // this file. The helper deletes the file + drops embeddings
+      // + sweeps every other wiki .md to clean stale body
+      // wikilinks, index.md listings, AND `related:` frontmatter
+      // arrays. The previous inline cleanup loop did 1 and 2 but
+      // left `related:` slugs pointing at deleted pages, which
+      // FrontmatterPanel renders as a broken-ref warning icon.
+      const { cascadeDeleteWikiPagesWithRefs } = await import(
+        "@/lib/wiki-page-delete"
+      )
+      const cascadeResult =
+        pagesToDelete.length > 0
+          ? await cascadeDeleteWikiPagesWithRefs(pp, pagesToDelete)
+          : { deletedPaths: [], rewrittenFiles: 0 }
+      const actuallyDeleted = cascadeResult.deletedPaths
 
     // Step 7: Append deletion record to log.md
     try {
@@ -803,14 +763,3 @@ function DeleteButton({
   )
 }
 
-function flattenMdFiles(nodes: FileNode[]): FileNode[] {
-  const files: FileNode[] = []
-  for (const node of nodes) {
-    if (node.is_dir && node.children) {
-      files.push(...flattenMdFiles(node.children))
-    } else if (!node.is_dir && node.name.endsWith(".md")) {
-      files.push(node)
-    }
-  }
-  return files
-}