Fix #10: checkout sets the executable bit, and status/diff report mode changes

.changeset/checkout-exec-bit.md

@@ -0,0 +1,5 @@
+---
+"just-git": patch
+---
+
+Checkout applies the executable bit of `100755` entries through the new optional `FileSystem.chmod`, and `status`/`diff` report mode-only changes (`old mode 100755` / `new mode 100644`) instead of silently committing them.

docs/FILE_REFERENCE.md

@@ -97,7 +97,7 @@ Exported symbols from `src/lib/`. Generated by `bun scripts/gen-lib-reference.ts
 
 ### lib/index.ts
 
-- `getIndexTimestamp`, `readIndex`, `writeIndex`, `addEntry`, `removeEntry`, `findEntry`, `hasConflicts`, `getConflictedPaths`, `getStage0Entries`, `clearIndex`, `buildIndex`, `defaultStat`, `indexStatFromFileStat`, `indexStatMatchesFile`, `gitModeFromFileStat`, `refreshIndexStatsAfterCheckout`
+- `getIndexTimestamp`, `readIndex`, `writeIndex`, `addEntry`, `removeEntry`, `findEntry`, `hasConflicts`, `getConflictedPaths`, `getStage0Entries`, `clearIndex`, `buildIndex`, `defaultStat`, `indexStatFromFileStat`, `indexStatMatchesFile`, `gitModeFromFileStat`, `worktreeMode`, `refreshIndexStatsAfterCheckout`
 
 ### lib/log-format.ts
 
@@ -250,7 +250,7 @@ Exported symbols from `src/lib/`. Generated by `bun scripts/gen-lib-reference.ts
 
 ### lib/symlink.ts
 
-- `lstatSafe`, `isSymlinkMode`, `isSubmoduleMode`, `readWorktreeContent`
+- `lstatSafe`, `isSymlinkMode`, `isExecutableMode`, `isRegularFileMode`, `isSubmoduleMode`, `readWorktreeContent`
 
 ### lib/tree-ops.ts
 

src/commands/diff.ts

@@ -229,15 +229,13 @@ async function collectUnstaged(
 		const indexEntry = stage0.get(diff.path);
 		if (!indexEntry) continue;
 
-		const oldMode = fmtMode(indexEntry.mode);
-
 		items.push({
 			path: diff.path,
 			status: diff.status === "deleted" ? "D" : "M",
 			oldHash: indexEntry.hash,
 			newHash: diff.worktreeHash,
-			oldMode,
-			newMode: oldMode,
+			oldMode: fmtMode(indexEntry.mode),
+			newMode: fmtMode(diff.worktreeMode ?? indexEntry.mode),
 			newFromWorkTree: diff.status === "modified",
 		});
 	}
@@ -390,7 +388,7 @@ async function collectCached(
 				newHash: entry.hash,
 				newMode: fmtMode(entry.mode),
 			});
-		} else if (baseEntry.hash !== entry.hash) {
+		} else if (baseEntry.hash !== entry.hash || Number.parseInt(baseEntry.mode, 8) !== entry.mode) {
 			diffs.push({
 				path,
 				status: "modified",
@@ -585,7 +583,7 @@ async function collectCommitToWorkTree(
 
 		const effectiveHash =
 			workTreeDiff?.status === "modified" ? workTreeDiff.worktreeHash : indexEntry.hash;
-		const effectiveMode = fmtMode(indexEntry.mode);
+		const effectiveMode = fmtMode(workTreeDiff?.worktreeMode ?? indexEntry.mode);
 		if (effectiveHash !== entry.hash || effectiveMode !== entry.mode) {
 			items.push({
 				path,

src/commands/mv.ts

@@ -200,7 +200,9 @@ export function registerMvCommand(parent: Command, ext?: GitExtensions) {
 				}
 
 				const content = await ctx.fs.readFileBuffer(move.srcAbs);
+				const srcMode = (await ctx.fs.stat(move.srcAbs)).mode;
 				await ctx.fs.writeFile(move.dstAbs, content);
+				if (ctx.fs.chmod) await ctx.fs.chmod(move.dstAbs, srcMode & 0o7777);
 				await ctx.fs.rm(move.srcAbs);
 
 				// 2. Update the index: remove old entry, add new entry

src/fs.ts

@@ -38,7 +38,9 @@ export interface FileStat {
  *
  * The three optional symlink methods (`lstat`, `readlink`, `symlink`) enable
  * symlink support. When omitted, symlinks degrade to plain files containing
- * the target path as content (`core.symlinks=false` behavior).
+ * the target path as content (`core.symlinks=false` behavior). The optional
+ * `chmod` lets checkout apply the executable bit of `100755` entries; when
+ * omitted, every file is checked out non-executable.
  *
  * See {@link MemoryFileSystem} for a ready-made in-memory implementation.
  */
@@ -98,6 +100,13 @@ export interface FileSystem {
 	 * @throws Error if `path` already exists.
 	 */
 	symlink?(target: string, path: string): Promise<void>;
+	/**
+	 * Set the permission bits of a file (e.g. `0o755`), following symlinks.
+	 * Checkout uses this to apply or clear the executable bit; without it,
+	 * a `100755` blob is checked out as `100644`.
+	 * @throws Error if the path doesn't exist.
+	 */
+	chmod?(path: string, mode: number): Promise<void>;
 	/**
 	 * Move/rename a file or directory from `src` to `dest`.
 	 *

src/lib/command-utils.ts

@@ -214,14 +214,18 @@ export async function requireAuthor(
  * Compares stage-0 index entries against the tree map for modifications,
  * additions, and deletions.
  */
-export function hasStagedChanges(index: Index, headMap: Map<string, { hash: string }>): boolean {
-	const stage0 = new Map<string, { hash: string }>();
+export function hasStagedChanges(
+	index: Index,
+	headMap: Map<string, { hash: string; mode: string }>,
+): boolean {
+	const stage0 = new Map<string, { hash: string; mode: number }>();
 	for (const e of index.entries) {
 		if (e.stage === 0) stage0.set(e.path, e);
 	}
 	for (const [path, entry] of stage0) {
 		const headEntry = headMap.get(path);
 		if (!headEntry || headEntry.hash !== entry.hash) return true;
+		if (Number.parseInt(headEntry.mode, 8) !== entry.mode) return true;
 	}
 	for (const [path] of headMap) {
 		if (!stage0.has(path)) return true;

src/lib/diff-algorithm.ts

@@ -1169,6 +1169,10 @@ function formatHashForIndexLine(hash?: string): string {
 	return abbreviateHash(hash);
 }
 
+function hasModeChange(opts: FormatOptions): boolean {
+	return !!opts.oldMode && !!opts.newMode && opts.oldMode !== opts.newMode;
+}
+
 function pushDiffGitHeader(
 	out: string[],
 	opts: FormatOptions,
@@ -1199,7 +1203,7 @@ function formatBinaryDiff(opts: FormatOptions, oldIsBinary: boolean, newIsBinary
 	const newPath = opts.renameTo ?? path;
 	const isNew = opts.isNew ?? oldContent === "";
 	const isDeleted = opts.isDeleted ?? newContent === "";
-	if (oldContent === newContent && !isRename) return "";
+	if (oldContent === newContent && !isRename && !hasModeChange(opts)) return "";
 
 	const out: string[] = [];
 	pushDiffGitHeader(out, opts, newPath, isNew, isDeleted, isRename);
@@ -1281,15 +1285,14 @@ export function formatUnifiedDiff(opts: FormatOptions): string {
 	}
 	const hunks = buildHunks(edits, opts.contextLines);
 
-	if (hunks.length === 0 && !isRename) return "";
+	if (hunks.length === 0 && !isRename && !hasModeChange(opts)) return "";
 
 	const isNew = opts.isNew ?? oldContent === "";
 	const isDeleted = opts.isDeleted ?? newContent === "";
 
 	const out: string[] = [];
 	pushDiffGitHeader(out, opts, newPath, isNew, isDeleted, isRename);
 
-	// For exact renames with no content change, stop here
 	if (hunks.length === 0) {
 		return `${out.join("\n")}\n`;
 	}

src/lib/index.ts

@@ -1,9 +1,9 @@
-import type { FileStat } from "../fs.ts";
+import type { FileStat, FileSystem } from "../fs.ts";
 import { bytesToHex, hexToBytes } from "./hex.ts";
 import { verifyPath } from "./path-safety.ts";
 import { join } from "./path.ts";
 import { sha1 } from "./sha1.ts";
-import { isSubmoduleMode, lstatSafe } from "./symlink.ts";
+import { isRegularFileMode, isSubmoduleMode, isSymlinkMode, lstatSafe } from "./symlink.ts";
 import type { GitContext, Index, IndexEntry, IndexStat } from "./types.ts";
 
 // ── Constants ───────────────────────────────────────────────────────
@@ -192,13 +192,14 @@ export function indexStatFromFileStat(stat: FileStat, size: number = stat.size):
  * and must still be hashed.
  */
 export function indexStatMatchesFile(
+	fs: FileSystem,
 	entry: IndexEntry,
 	stat: FileStat,
 	indexTimestamp: Date | undefined,
 ): boolean {
 	if (!indexTimestamp || !stat.isFile || stat.isSymbolicLink) return false;
 	if (entry.stat.mtimeSeconds === 0 || stat.size < 0 || stat.size > 0xffffffff) return false;
-	if (gitModeFromFileStat(stat) !== entry.mode || stat.size !== entry.stat.size) return false;
+	if (worktreeMode(fs, entry, stat) !== entry.mode || stat.size !== entry.stat.size) return false;
 
 	const fileMtimeMs = timestampMilliseconds(stat.mtime);
 	const indexMtimeMs = timestampMilliseconds(indexTimestamp);
@@ -231,6 +232,30 @@ export function gitModeFromFileStat(stat: FileStat): number {
 	return stat.mode & 0o111 ? 0o100755 : 0o100644;
 }
 
+function fileStandsInForSymlink(
+	fs: FileSystem,
+	entry: Pick<IndexEntry, "mode">,
+	stat: FileStat,
+): boolean {
+	return stat.isFile && isSymlinkMode(entry.mode) && !fs.symlink;
+}
+
+function fsTracksExecutableBit(fs: FileSystem): boolean {
+	return fs.chmod !== undefined;
+}
+
+export function worktreeMode(
+	fs: FileSystem,
+	entry: Pick<IndexEntry, "mode"> | undefined,
+	stat: FileStat,
+): number {
+	if (entry && fileStandsInForSymlink(fs, entry, stat)) return entry.mode;
+	if (stat.isFile && !fsTracksExecutableBit(fs)) {
+		return entry && isRegularFileMode(entry.mode) ? entry.mode : 0o100644;
+	}
+	return gitModeFromFileStat(stat);
+}
+
 /**
  * Refresh stat metadata for index entries whose content a caller has just
  * materialized in the worktree. Paths that cannot be verified by type/mode
@@ -256,7 +281,7 @@ export async function refreshIndexStatsAfterCheckout(
 		}
 
 		const stat = await lstatSafe(ctx.fs, join(ctx.workTree, entry.path)).catch(() => null);
-		if (!stat || gitModeFromFileStat(stat) !== entry.mode) {
+		if (!stat || worktreeMode(ctx.fs, entry, stat) !== entry.mode) {
 			entries.push(entry);
 			continue;
 		}

src/lib/status-format.ts

@@ -452,7 +452,7 @@ export async function getStagedChanges(
 				newHash: entry.hash,
 				newMode: entry.mode.toString(8).padStart(6, "0"),
 			});
-		} else if (headEntry.hash !== entry.hash) {
+		} else if (headEntry.hash !== entry.hash || Number.parseInt(headEntry.mode, 8) !== entry.mode) {
 			rawDiffs.push({
 				path,
 				status: "modified",

src/lib/symlink.ts

@@ -13,6 +13,16 @@ export function isSymlinkMode(mode: number | string): boolean {
 	return mode === 0o120000;
 }
 
+export function isExecutableMode(mode: number | string): boolean {
+	if (typeof mode === "string") return mode === "100755";
+	return mode === 0o100755;
+}
+
+export function isRegularFileMode(mode: number | string): boolean {
+	if (typeof mode === "string") return mode === "100644" || mode === "100755";
+	return mode === 0o100644 || mode === 0o100755;
+}
+
 /** Check whether a git mode (numeric or string) represents a submodule (gitlink). */
 export function isSubmoduleMode(mode: number | string): boolean {
 	if (typeof mode === "string") return mode === "160000";

src/lib/types.ts

@@ -302,4 +302,5 @@ export interface WorkTreeDiff {
 	indexHash?: ObjectId;
 	/** Hash computed from modified worktree content during comparison. */
 	worktreeHash?: ObjectId;
+	worktreeMode?: number;
 }