diff --git a/packages/cli/src/parse.ts b/packages/cli/src/parse.ts
index c0409b9de3..cf6d96589a 100644
--- a/packages/cli/src/parse.ts
+++ b/packages/cli/src/parse.ts
@@ -2,9 +2,14 @@ import replaceExt from "replace-ext"
 import { readFile } from "node:fs/promises"
 import { DOCXTryParse } from "../../core/src/docx"
 import { extractFenced } from "../../core/src/fence"
-import { expandFiles, writeText, readText } from "../../core/src/fs"
+import {
+    expandFiles,
+    writeText,
+    readText,
+    tryReadText,
+} from "../../core/src/fs"
 import { HTMLToText } from "../../core/src/html"
-import { isJSONLFilename, readJSONL } from "../../core/src/jsonl"
+import { isJSONLFilename, JSONLTryParse } from "../../core/src/jsonl"
 import { parsePdf } from "../../core/src/pdf"
 import { estimateTokens } from "../../core/src/tokens"
 import { YAMLStringify } from "../../core/src/yaml"
@@ -12,6 +17,7 @@ import { resolveTokenEncoder } from "../../core/src/encoders"
 import { DEFAULT_MODEL } from "../../core/src/constants"
 import { promptyParse, promptyToGenAIScript } from "../../core/src/prompty"
 import { basename, join } from "node:path"
+import { JSONLLMTryParse } from "../../core/src/json5"
 
 export async function parseFence(language: string, file: string) {
     const res = await parsePdf(file)
@@ -44,7 +50,8 @@ export async function jsonl2json(files: string[]) {
             console.log(`skipping ${file}`)
             continue
         }
-        const objs = await readJSONL(file)
+        const content = await tryReadText(file)
+        const objs = await JSONLTryParse(content, { repair: true })
         const out = replaceExt(file, ".json")
         await writeText(out, JSON.stringify(objs, null, 2))
         console.log(`${file} -> ${out}`)
diff --git a/packages/core/src/cache.ts b/packages/core/src/cache.ts
index e9ddc0f408..a782533f2b 100644
--- a/packages/core/src/cache.ts
+++ b/packages/core/src/cache.ts
@@ -1,10 +1,12 @@
 // Import necessary modules and types
-import { appendJSONL, readJSONL, writeJSONL } from "./jsonl"
-import { host, runtimeHost } from "./host"
+import { appendJSONL, JSONLTryParse, writeJSONL } from "./jsonl"
+import { host } from "./host"
 import { dotGenaiscriptPath, sha256string } from "./util"
 import { CHANGE } from "./constants"
 import { TraceOptions } from "./trace"
 import { CORE_VERSION } from "./version"
+import { tryReadText } from "./fs"
+import { JSON5TryParse } from "./json5"
 
 /**
  * Represents a cache entry with a hashed identifier (`sha`), `key`, and `val`.
@@ -60,7 +62,8 @@ export class JSONLineCache<K, V> extends EventTarget {
         if (this._entries) return
         this._entries = {}
         await host.createDirectory(this.folder()) // Ensure directory exists
-        const objs: CacheEntry<K, V>[] = await readJSONL(this.path())
+        const content = await tryReadText(this.path())
+        const objs: CacheEntry<K, V>[] = (await JSON5TryParse(content)) ?? []
         let numdup = 0 // Counter for duplicates
         for (const obj of objs) {
             if (this._entries[obj.sha]) numdup++ // Count duplicates
diff --git a/packages/core/src/jsonl.ts b/packages/core/src/jsonl.ts
index 0900ceafe2..fe38e5fab3 100644
--- a/packages/core/src/jsonl.ts
+++ b/packages/core/src/jsonl.ts
@@ -13,31 +13,6 @@ export function isJSONLFilename(fn: string) {
     return /\.(jsonl|mdjson|ldjson)$/i.test(fn)
 }
 
-export async function readJSONL(fn: string) {
-    const buf = await tryReadFile(fn)
-    const res: any[] = []
-    if (buf == null) return res
-    let line = 1
-    let numerr = 0
-    const decoder = host.createUTF8Decoder()
-    for (let pos = 0; pos < buf.length; ) {
-        let ep = buf.indexOf(10, pos)
-        if (ep < 0) ep = buf.length
-        const str = decoder.decode(buf.slice(pos, ep))
-        if (!/^\s*$/.test(str)) {
-            try {
-                res.push(JSON.parse(str))
-            } catch (e) {
-                if (!numerr) logWarn(`${fn}(${line}): JSON error`)
-                numerr++
-            }
-        }
-        pos = ep + 1
-        line++
-    }
-    return res
-}
-
 export function JSONLTryParse(
     text: string,
     options?: {
@@ -49,7 +24,7 @@ export function JSONLTryParse(
     for (const line of text.split("\n")) {
         if (!line) continue
         const obj = JSON5TryParse(line, options)
-        res.push(obj)
+        if (obj !== undefined && obj !== null) res.push(obj)
     }
     return res
 }
@@ -57,7 +32,7 @@ export function JSONLTryParse(
 export function JSONLStringify(objs: any[]) {
     const acc: string[] = []
     if (objs?.length)
-        for (const o of objs) {
+        for (const o of objs.filter((o) => o !== undefined && o !== null)) {
             const s = JSON.stringify(o)
             acc.push(s)
         }
diff --git a/packages/vscode/genaisrc/cmt.genai.mts b/packages/vscode/genaisrc/cmt.genai.mts
index 10728324eb..6a9262f58d 100644
--- a/packages/vscode/genaisrc/cmt.genai.mts
+++ b/packages/vscode/genaisrc/cmt.genai.mts
@@ -21,8 +21,6 @@ script({
 const { format, build } = env.vars
 const saveLimit = pLimit(1)
 
-console.log({ format, build })
-
 // Get files from environment or modified files from Git if none provided
 let files = env.files
 if (files.length === 0) {
@@ -122,7 +120,8 @@ You should analyze it, and add/update appropriate comments as needed.
 To add or update comments to this code, follow these steps:
 
 1. Analyze the code to understand its structure and functionality.
-- If you are not familiar with the programming language, ignore the file.
+- If you are not familiar with the programming language, emit an empty file.
+- If there is no code, emit an empty file.
 2. Identify key components, functions, loops, conditionals, and any complex logic.
 3. Add comments that explain:
 - The purpose of functions or code blocks using the best comment format for that programming language.
@@ -158,7 +157,7 @@ Your comments should provide insight into the code's purpose, logic, and any imp
         )
         const { text, fences } = res
         const newContent = fences?.[0]?.content ?? text
-        if (!newContent) return undefined
+        if (!newContent?.trim()) return undefined
         if (newContent === content) break
         content = newContent
     }