fix: include previously-indexed files in incremental and --files modes (audit #2/#12)

getChangedFiles() hard-filtered by LANG_MAP, silently dropping custom-
extension files that were indexed during --full. Now also accepts files
already in the files table. --files mode no longer rejects non-standard
extensions — warns instead and indexes as text.

Author: SutuSebastian

src/application/index-engine.ts

@@ -126,10 +126,11 @@ export function getChangedFiles(db: CodemapDatabase): {
       .filter(Boolean)
       .map((line: string) => line.slice(3).trim());
 
+    const indexedPaths = new Set(getAllFileHashes(db).keys());
     const allChanged = [...new Set([...diffFiles, ...statusFiles])].filter(
       (f) => {
         const ext = extname(f);
-        return ext in LANG_MAP;
+        return ext in LANG_MAP || indexedPaths.has(f);
       },
     );
 

src/application/run-index.ts

@@ -1,5 +1,3 @@
-import { extname } from "node:path";
-
 import { createSchema, getAllFileHashes, setMeta } from "../db";
 import type { CodemapDatabase } from "../db";
 import {
@@ -9,7 +7,6 @@ import {
   getCurrentCommit,
   indexFiles,
   targetedReindex,
-  VALID_EXTENSIONS,
 } from "./index-engine";
 import type { IndexResult, IndexTableStats } from "./types";
 
@@ -82,10 +79,7 @@ export async function runCodemapIndex(
   }
 
   if (mode === "files") {
-    const targetFiles = (options.files ?? []).filter((f) => {
-      const ext = extname(f);
-      return VALID_EXTENSIONS.has(ext);
-    });
+    const targetFiles = options.files ?? [];
     if (targetFiles.length === 0) {
       return {
         mode: "files",

src/cli/cmd-index.ts

@@ -20,14 +20,12 @@ export async function runIndexCmd(opts: {
   const db = openDb();
   try {
     if (args[0] === "--files" && args.length > 1) {
-      const targetFiles = args.slice(1).filter((f) => {
-        const ext = extname(f);
-        if (!VALID_EXTENSIONS.has(ext)) {
-          console.warn(`  Skipping ${f}: unsupported extension "${ext}"`);
-          return false;
+      const targetFiles = args.slice(1);
+      for (const f of targetFiles) {
+        if (!VALID_EXTENSIONS.has(extname(f))) {
+          console.warn(`  ${f}: non-standard extension, indexing as text`);
         }
-        return true;
-      });
+      }
       if (targetFiles.length > 0) {
         await runCodemapIndex(db, {
           mode: "files",