core: prevent file deletion when reverting changes to existing files

packages/opencode/src/snapshot/index.ts

@@ -105,8 +105,17 @@ export namespace Snapshot {
           .cwd(Instance.worktree)
           .nothrow()
         if (result.exitCode !== 0) {
-          log.info("file not found in history, deleting", { file })
-          await fs.unlink(file).catch(() => {})
+          const relativePath = path.relative(Instance.worktree, file)
+          const checkTree = await $`git --git-dir=${git} ls-tree ${item.hash} -- ${relativePath}`
+            .quiet()
+            .cwd(Instance.worktree)
+            .nothrow()
+          if (checkTree.exitCode === 0 && checkTree.text().trim()) {
+            log.info("file existed in snapshot but checkout failed, keeping", { file })
+          } else {
+            log.info("file did not exist in snapshot, deleting", { file })
+            await fs.unlink(file).catch(() => {})
+          }
         }
         files.add(file)
       }

packages/opencode/test/snapshot/snapshot.test.ts

@@ -532,3 +532,55 @@ test("restore function", async () => {
     },
   })
 })
+
+test("revert should not delete files that existed but were deleted in snapshot", async () => {
+  await using tmp = await bootstrap()
+  await Instance.provide({
+    directory: tmp.path,
+    fn: async () => {
+      const snapshot1 = await Snapshot.track()
+      expect(snapshot1).toBeTruthy()
+
+      await $`rm ${tmp.path}/a.txt`.quiet()
+
+      const snapshot2 = await Snapshot.track()
+      expect(snapshot2).toBeTruthy()
+
+      await Bun.write(`${tmp.path}/a.txt`, "recreated content")
+
+      const patch = await Snapshot.patch(snapshot2!)
+      expect(patch.files).toContain(`${tmp.path}/a.txt`)
+
+      await Snapshot.revert([patch])
+
+      expect(await Bun.file(`${tmp.path}/a.txt`).exists()).toBe(false)
+    },
+  })
+})
+
+test("revert preserves file that existed in snapshot when deleted then recreated", async () => {
+  await using tmp = await bootstrap()
+  await Instance.provide({
+    directory: tmp.path,
+    fn: async () => {
+      await Bun.write(`${tmp.path}/existing.txt`, "original content")
+
+      const snapshot = await Snapshot.track()
+      expect(snapshot).toBeTruthy()
+
+      await $`rm ${tmp.path}/existing.txt`.quiet()
+      await Bun.write(`${tmp.path}/existing.txt`, "recreated")
+      await Bun.write(`${tmp.path}/newfile.txt`, "new")
+
+      const patch = await Snapshot.patch(snapshot!)
+      expect(patch.files).toContain(`${tmp.path}/existing.txt`)
+      expect(patch.files).toContain(`${tmp.path}/newfile.txt`)
+
+      await Snapshot.revert([patch])
+
+      expect(await Bun.file(`${tmp.path}/newfile.txt`).exists()).toBe(false)
+      expect(await Bun.file(`${tmp.path}/existing.txt`).exists()).toBe(true)
+      expect(await Bun.file(`${tmp.path}/existing.txt`).text()).toBe("original content")
+    },
+  })
+})