fix: remaining low-severity bugs from clawpatch review

Author: SutuSebastian

.changeset/fix-high-bugs-batch.md

@@ -2,4 +2,4 @@
 "codemap": patch
 ---
 
-Fix high-severity bugs (describe.each parent stack, git porcelain -z paths, CLI symlink entry, pr-comment TTY stdin) and medium bugs (changed-since -z paths, perf baseline RUNS guard, qualified typeof, decorator args_text, for-of binding refs, HTTP body drain, benchmark regex validation, jsx INSERT RETURNING id, sqlite stmt cache on close).
+Fix high-severity bugs (describe.each parent stack, git porcelain -z paths, CLI symlink entry, pr-comment TTY stdin), medium bugs (changed-since -z paths, perf baseline RUNS guard, qualified typeof, decorator args_text, for-of binding refs, HTTP body drain, benchmark regex validation, jsx INSERT RETURNING id, sqlite stmt cache on close), and low bugs (CLI parse guards, incremental delete transaction, apply summary.files, extension case, pnpm # paths, coverage db.transaction, impact walk delimiter, worker errors, pointer dedup, benchmark readAll visibility).

src/adapters/builtin.test.ts

@@ -5,6 +5,7 @@ import { BUILTIN_ADAPTERS, getAdapterForExtension } from "./builtin";
 describe("getAdapterForExtension", () => {
   it("resolves TS/JS extensions to builtin.ts-js", () => {
     expect(getAdapterForExtension(".ts")?.id).toBe("builtin.ts-js");
+    expect(getAdapterForExtension(".TS")?.id).toBe("builtin.ts-js");
     expect(getAdapterForExtension(".tsx")?.id).toBe("builtin.ts-js");
   });
 

src/adapters/builtin.ts

@@ -109,7 +109,8 @@ function buildAdapterIndex(
   // First-match-wins: skip ext if an earlier adapter already claimed it.
   for (const a of adapters) {
     for (const ext of a.extensions) {
-      if (!index.has(ext)) index.set(ext, a);
+      const key = ext.toLowerCase();
+      if (!index.has(key)) index.set(key, a);
     }
   }
   return index;
@@ -129,5 +130,5 @@ export function getAdapterForExtension(
     index = buildAdapterIndex(adapters);
     adapterIndexCache.set(adapters, index);
   }
-  return index.get(ext);
+  return index.get(ext.toLowerCase());
 }

src/agents-init.test.ts

@@ -369,6 +369,31 @@ describe("upsertCodemapPointerFile", () => {
     }
   });
 
+  it("replaces ALL managed sections when file has two blocks", () => {
+    const dir = mkdtempSync(join(tmpdir(), "codemap-pointer-"));
+    const p = join(dir, "NOTE.md");
+    try {
+      writeFileSync(
+        p,
+        `${wrapPointerTest("FIRST")}\nOther content\n${wrapPointerTest("SECOND")}`,
+        "utf-8",
+      );
+      upsertCodemapPointerFile(
+        p,
+        "UPDATED\n\nstill https://github.com/stainless-code/codemap\n`.agents/skills/codemap`\n`codemap query`",
+        "NOTE.md",
+        false,
+      );
+      const out = readFileSync(p, "utf-8");
+      expect(out).toContain("UPDATED");
+      expect(out).not.toContain("FIRST");
+      expect(out).not.toContain("SECOND");
+      expect(out.match(new RegExp(CODMAP_POINTER_BEGIN, "g"))?.length).toBe(1);
+    } finally {
+      rmSync(dir, { recursive: true, force: true });
+    }
+  });
+
   it("--force replaces entire file with managed section", () => {
     const dir = mkdtempSync(join(tmpdir(), "codemap-pointer-"));
     const p = join(dir, "AGENTS.md");

src/agents-init.ts

@@ -197,10 +197,10 @@ function escapeRegexChars(s: string): string {
   return s.replace(/[.*+?^${}()|[\]\\]/g, "\\$&");
 }
 
-function codemapPointerBlockRegex(): RegExp {
+function codemapPointerBlockRegex(flags = "m"): RegExp {
   return new RegExp(
     `${escapeRegexChars(CODMAP_POINTER_BEGIN)}\\s*[\\s\\S]*?${escapeRegexChars(CODMAP_POINTER_END)}`,
-    "m",
+    flags,
   );
 }
 
@@ -247,10 +247,15 @@ export function upsertCodemapPointerFile(
   }
 
   const content = readFileSync(path, "utf-8");
-  const re = codemapPointerBlockRegex();
 
-  if (content.match(re)) {
-    const next = content.replace(re, wrapped);
+  if (content.match(codemapPointerBlockRegex())) {
+    const stripped = content
+      .replace(codemapPointerBlockRegex("gm"), "")
+      .replace(/\n{3,}/g, "\n\n")
+      .trimEnd();
+    const sep = stripped.length === 0 || stripped.endsWith("\n") ? "" : "\n\n";
+    const next =
+      stripped.length === 0 ? wrapped : `${stripped}${sep}${wrapped}`;
     if (next === content) {
       console.log(`  Codemap section in ${label} already up to date`);
       return;

src/application/apply-engine.test.ts

@@ -753,6 +753,7 @@ describe("applyDiffPayload", () => {
       });
 
       expect(result.summary.rows).toBe(0); // row silently dropped
+      expect(result.summary.files).toBe(0);
       expect(result.files).toEqual([]);
     });
   });

src/application/apply-engine.ts

@@ -133,6 +133,7 @@ export function applyDiffPayload(opts: ApplyDiffPayloadOpts): ApplyJsonPayload {
   // would split phase 2 mid-loop and leak Q2 (c) all-or-nothing.
   const seenLines = new Map<string, Set<number>>();
   let validRows = 0;
+  const distinctInputFiles = new Set<string>();
 
   for (const row of rows) {
     const filePath = readString(row, "file_path");
@@ -151,6 +152,11 @@ export function applyDiffPayload(opts: ApplyDiffPayloadOpts): ApplyJsonPayload {
       continue;
     }
     validRows++;
+    distinctInputFiles.add(
+      isAbsolute(filePath) || !isWithinProjectRoot(resolvedRoot, filePath)
+        ? filePath
+        : canonicalizeProjectFilePath(resolvedRoot, filePath),
+    );
 
     // Path-containment guard — without it `file_path: "../escape.ts"` would
     // write sibling-of-root files (CLI + MCP + HTTP all share this engine).
@@ -261,20 +267,6 @@ export function applyDiffPayload(opts: ApplyDiffPayloadOpts): ApplyJsonPayload {
   }
 
   const filesWithConflicts = new Set(conflicts.map((c) => c.file_path)).size;
-  const distinctInputFiles = new Set<string>();
-  for (const row of rows) {
-    const filePath = readString(row, "file_path");
-    if (filePath === undefined) continue;
-    // Count distinct disk targets, not distinct spellings — same as the
-    // dedup applied to the cache + pending keys.
-    if (isAbsolute(filePath) || !isWithinProjectRoot(resolvedRoot, filePath)) {
-      distinctInputFiles.add(filePath);
-    } else {
-      distinctInputFiles.add(
-        canonicalizeProjectFilePath(resolvedRoot, filePath),
-      );
-    }
-  }
 
   // Q2 (c) — any conflict aborts the run; dry-run never writes. Same Q5 envelope.
   if (dryRun || conflicts.length > 0) {

src/application/coverage-engine.ts

@@ -144,8 +144,7 @@ export function upsertCoverageRows(opts: UpsertOpts): IngestResult {
   // we're ingesting (a re-ingest is a full replace per file, not a merge),
   // then bulk-insert the new aggregates. Idempotent across re-runs.
   let pruned = 0;
-  db.run("BEGIN");
-  try {
+  const persist = db.transaction(() => {
     for (const file_path of filesSeen) {
       db.run("DELETE FROM coverage WHERE file_path = ?", [file_path]);
     }
@@ -203,12 +202,8 @@ export function upsertCoverageRows(opts: UpsertOpts): IngestResult {
       "coverage_last_ingested_format",
       format,
     ]);
-
-    db.run("COMMIT");
-  } catch (err) {
-    db.run("ROLLBACK");
-    throw err;
-  }
+  });
+  persist();
 
   return {
     ingested: { symbols: buckets.size, files: filesSeen.size },

src/application/impact-engine.ts

@@ -290,14 +290,14 @@ function walkCalls(db: CodemapDatabase, opts: WalkOpts): ImpactNode[] {
   // Seed depth = 0; `WHERE depth > 0` filters seed; `< depthLimit` is the cap.
   const sql = `
     WITH RECURSIVE walk(node, depth, path, file_path) AS (
-      SELECT ?, 0, ',' || ? || ',', NULL
+      SELECT ?, 0, char(30) || ? || char(30), NULL
       UNION ALL
       SELECT c.${joinToCol}, walk.depth + 1,
-             walk.path || c.${joinToCol} || ',', c.file_path
+             walk.path || c.${joinToCol} || char(30), c.file_path
       FROM calls c
       JOIN walk ON c.${joinFromCol} = walk.node
       WHERE walk.depth < ?
-        AND instr(walk.path, ',' || c.${joinToCol} || ',') = 0
+        AND instr(walk.path, char(30) || c.${joinToCol} || char(30)) = 0
     )
     SELECT node, depth, file_path
     FROM (
@@ -359,14 +359,14 @@ function walkFileGraph(db: CodemapDatabase, opts: WalkOpts): ImpactNode[] {
 
   const sql = `
     WITH RECURSIVE walk(node, depth, path) AS (
-      SELECT ?, 0, ',' || ? || ','
+      SELECT ?, 0, char(30) || ? || char(30)
       UNION ALL
       SELECT c.${joinToCol}, walk.depth + 1,
-             walk.path || c.${joinToCol} || ','
+             walk.path || c.${joinToCol} || char(30)
       FROM ${table} c
       JOIN walk ON c.${joinFromCol} = walk.node
       WHERE walk.depth < ?
-        AND instr(walk.path, ',' || c.${joinToCol} || ',') = 0
+        AND instr(walk.path, char(30) || c.${joinToCol} || char(30)) = 0
         ${filterNonNull}
     )
     SELECT node, MIN(depth) AS depth

src/application/index-engine.ts

@@ -91,11 +91,11 @@ const TS_EXTENSIONS = new Set([
 const CSS_EXTENSIONS = new Set([".css"]);
 
 function langFromExt(ext: string): string {
-  return LANG_MAP[ext] ?? "text";
+  return LANG_MAP[ext.toLowerCase()] ?? "text";
 }
 
 function fileCategory(path: string): "ts" | "css" | "text" {
-  const ext = extname(path);
+  const ext = extname(path).toLowerCase();
   if (TS_EXTENSIONS.has(ext)) return "ts";
   if (CSS_EXTENSIONS.has(ext)) return "css";
   return "text";
@@ -424,6 +424,8 @@ export async function indexFiles(
     sourceCache?: ChangedSourceCache;
     /** When set, incremental branch skips its own `getAllFileHashes(db)` call. */
     existingHashes?: Map<string, string>;
+    /** When set, incremental branch deletes these paths inside the same transaction as re-indexing. */
+    deletedPaths?: string[];
   },
 ): Promise<IndexRunStats> {
   const quiet = options?.quiet ?? false;
@@ -485,6 +487,10 @@ export async function indexFiles(
     const sourceCache = options?.sourceCache;
 
     const transaction = db.transaction(() => {
+      const deleted = options?.deletedPaths ?? [];
+      if (deleted.length > 0) {
+        deleteFilesFromIndex(db, deleted, quiet);
+      }
       for (const relPath of filePaths) {
         const absPath = join(root, relPath);
         let source: string;