fix(opencode): Use standard resolve function to get proper filePaths for tools

packages/opencode/src/tool/apply_patch.ts

@@ -13,6 +13,7 @@ import { LSP } from "../lsp"
 import { AppFileSystem } from "@opencode-ai/shared/filesystem"
 import DESCRIPTION from "./apply_patch.txt"
 import { File } from "../file"
+import { relative } from "./relative"
 import { Format } from "../format"
 
 const PatchParams = z.object({
@@ -177,7 +178,7 @@ export const ApplyPatchTool = Tool.define(
       // Build per-file metadata for UI rendering (used for both permission and result)
       const files = fileChanges.map((change) => ({
         filePath: change.filePath,
-        relativePath: path.relative(Instance.worktree, change.movePath ?? change.filePath).replaceAll("\\", "/"),
+        relativePath: relative(change.movePath ?? change.filePath).replaceAll("\\", "/"),
         type: change.type,
         patch: change.diff,
         additions: change.additions,
@@ -186,7 +187,7 @@ export const ApplyPatchTool = Tool.define(
       }))
 
       // Check permissions if needed
-      const relativePaths = fileChanges.map((c) => path.relative(Instance.worktree, c.filePath).replaceAll("\\", "/"))
+      const relativePaths = fileChanges.map((c) => relative(c.filePath).replaceAll("\\", "/"))
       yield* ctx.ask({
         permission: "edit",
         patterns: relativePaths,
@@ -255,13 +256,13 @@ export const ApplyPatchTool = Tool.define(
       // Generate output summary
       const summaryLines = fileChanges.map((change) => {
         if (change.type === "add") {
-          return `A ${path.relative(Instance.worktree, change.filePath).replaceAll("\\", "/")}`
+          return `A ${relative(change.filePath).replaceAll("\\", "/")}`
         }
         if (change.type === "delete") {
-          return `D ${path.relative(Instance.worktree, change.filePath).replaceAll("\\", "/")}`
+          return `D ${relative(change.filePath).replaceAll("\\", "/")}`
         }
         const target = change.movePath ?? change.filePath
-        return `M ${path.relative(Instance.worktree, target).replaceAll("\\", "/")}`
+        return `M ${relative(target).replaceAll("\\", "/")}`
       })
       let output = `Success. Updated the following files:\n${summaryLines.join("\n")}`
 
@@ -270,7 +271,7 @@ export const ApplyPatchTool = Tool.define(
         const target = change.movePath ?? change.filePath
         const block = LSP.Diagnostic.report(target, diagnostics[AppFileSystem.normalizePath(target)] ?? [])
         if (!block) continue
-        const rel = path.relative(Instance.worktree, target).replaceAll("\\", "/")
+        const rel = relative(target).replaceAll("\\", "/")
         output += `\n\nLSP errors detected in ${rel}, please fix:\n${block}`
       }
 

packages/opencode/src/tool/edit.ts

@@ -17,6 +17,7 @@ import { Format } from "../format"
 import { Instance } from "../project/instance"
 import { Snapshot } from "@/snapshot"
 import { assertExternalDirectoryEffect } from "./external-directory"
+import { relative } from "./relative"
 import { AppFileSystem } from "@opencode-ai/shared/filesystem"
 
 function normalizeLineEndings(text: string): string {
@@ -64,6 +65,7 @@ export const EditTool = Tool.define(
             ? params.filePath
             : path.join(Instance.directory, params.filePath)
           yield* assertExternalDirectoryEffect(ctx, filePath)
+          const rel = relative(filePath)
 
           let diff = ""
           let contentOld = ""
@@ -75,7 +77,7 @@ export const EditTool = Tool.define(
               diff = trimDiff(createTwoFilesPatch(filePath, filePath, contentOld, contentNew))
               yield* ctx.ask({
                 permission: "edit",
-                patterns: [path.relative(Instance.worktree, filePath)],
+                patterns: [rel],
                 always: ["*"],
                 metadata: {
                   filepath: filePath,
@@ -171,7 +173,7 @@ export const EditTool = Tool.define(
               diff,
               filediff,
             },
-            title: `${path.relative(Instance.worktree, filePath)}`,
+            title: rel,
             output,
           }
         }),

packages/opencode/src/tool/multiedit.ts

@@ -3,8 +3,7 @@ import { Effect } from "effect"
 import * as Tool from "./tool"
 import { EditTool } from "./edit"
 import DESCRIPTION from "./multiedit.txt"
-import path from "path"
-import { Instance } from "../project/instance"
+import { relative } from "./relative"
 
 export const MultiEditTool = Tool.define(
   "multiedit",
@@ -49,7 +48,7 @@ export const MultiEditTool = Tool.define(
             results.push(result)
           }
           return {
-            title: path.relative(Instance.worktree, params.filePath),
+            title: relative(params.filePath),
             metadata: {
               results: results.map((r) => r.metadata),
             },

packages/opencode/src/tool/read.ts

@@ -11,6 +11,7 @@ import DESCRIPTION from "./read.txt"
 import { Instance } from "../project/instance"
 import { assertExternalDirectoryEffect } from "./external-directory"
 import { Instruction } from "../session/instruction"
+import { relative } from "./relative"
 
 const DEFAULT_READ_LIMIT = 2000
 const MAX_LINE_LENGTH = 2000
@@ -89,7 +90,7 @@ export const ReadTool = Tool.define(
       if (process.platform === "win32") {
         filepath = AppFileSystem.normalizePath(filepath)
       }
-      const title = path.relative(Instance.worktree, filepath)
+      const rel = relative(filepath)
 
       const stat = yield* fs.stat(filepath).pipe(
         Effect.catchIf(
@@ -105,7 +106,7 @@ export const ReadTool = Tool.define(
 
       yield* ctx.ask({
         permission: "read",
-        patterns: [filepath],
+        patterns: [rel],
         always: ["*"],
         metadata: {},
       })
@@ -121,7 +122,7 @@ export const ReadTool = Tool.define(
         const truncated = start + sliced.length < items.length
 
         return {
-          title,
+          title: rel,
           output: [
             `<path>${filepath}</path>`,
             `<type>directory</type>`,
@@ -148,7 +149,7 @@ export const ReadTool = Tool.define(
       if (isImage || isPdf) {
         const msg = `${isImage ? "Image" : "PDF"} read successfully`
         return {
-          title,
+          title: rel,
           output: msg,
           metadata: {
             preview: msg,
@@ -200,7 +201,7 @@ export const ReadTool = Tool.define(
       }
 
       return {
-        title,
+        title: rel,
         output,
         metadata: {
           preview: file.raw.slice(0, 20).join("\n"),

packages/opencode/src/tool/relative.ts

@@ -0,0 +1,7 @@
+import path from "path"
+import { Instance } from "../project/instance"
+
+export function relative(file: string) {
+  const root = Instance.worktree === "/" ? Instance.directory : Instance.worktree
+  return path.relative(root, file)
+}

packages/opencode/src/tool/write.ts

@@ -13,6 +13,7 @@ import { AppFileSystem } from "@opencode-ai/shared/filesystem"
 import { Instance } from "../project/instance"
 import { trimDiff } from "./edit"
 import { assertExternalDirectoryEffect } from "./external-directory"
+import { relative } from "./relative"
 
 const MAX_PROJECT_DIAGNOSTICS_FILES = 5
 
@@ -39,11 +40,11 @@ export const WriteTool = Tool.define(
 
           const exists = yield* fs.existsSafe(filepath)
           const contentOld = exists ? yield* fs.readFileString(filepath) : ""
-
+          const rel = relative(filepath)
           const diff = trimDiff(createTwoFilesPatch(filepath, filepath, contentOld, params.content))
           yield* ctx.ask({
             permission: "edit",
-            patterns: [path.relative(Instance.worktree, filepath)],
+            patterns: [rel],
             always: ["*"],
             metadata: {
               filepath,
@@ -78,7 +79,7 @@ export const WriteTool = Tool.define(
           }
 
           return {
-            title: path.relative(Instance.worktree, filepath),
+            title: rel,
             metadata: {
               diagnostics,
               filepath,

packages/opencode/test/tool/apply_patch.test.ts

@@ -175,6 +175,24 @@ describe("tool.apply_patch freeform", () => {
     })
   })
 
+  test("uses directory-relative permission paths in non-git projects", async () => {
+    await using fixture = await tmpdir()
+    const { ctx, calls } = makeCtx()
+
+    await Instance.provide({
+      directory: fixture.path,
+      fn: async () => {
+        const patchText = "*** Begin Patch\n*** Add File: .agents/new.txt\n+created\n*** End Patch"
+
+        await execute({ patchText }, ctx)
+
+        expect(calls).toHaveLength(1)
+        expect(calls[0]?.patterns).toEqual([".agents/new.txt"])
+        expect(calls[0]?.metadata.files[0]?.relativePath).toBe(".agents/new.txt")
+      },
+    })
+  })
+
   test("applies multiple hunks to one file", async () => {
     await using fixture = await tmpdir()
     const { ctx } = makeCtx()

packages/opencode/test/tool/edit.test.ts

@@ -126,6 +126,38 @@ describe("tool.edit", () => {
       })
     })
 
+    test("uses directory-relative permission paths in non-git projects", async () => {
+      await using tmp = await tmpdir()
+      const filepath = path.join(tmp.path, ".agents", "file.txt")
+      const calls: Array<{ patterns: readonly string[] }> = []
+
+      await Instance.provide({
+        directory: tmp.path,
+        fn: async () => {
+          const edit = await resolve()
+          await Effect.runPromise(
+            edit.execute(
+              {
+                filePath: filepath,
+                oldString: "",
+                newString: "new content",
+              },
+              {
+                ...ctx,
+                ask: (input) =>
+                  Effect.sync(() => {
+                    calls.push({ patterns: input.patterns })
+                  }),
+              },
+            ),
+          )
+
+          expect(calls).toHaveLength(1)
+          expect(calls[0]?.patterns).toEqual([path.join(".agents", "file.txt")])
+        },
+      })
+    })
+
     test("emits add event for new files", async () => {
       await using tmp = await tmpdir()
       const filepath = path.join(tmp.path, "new.txt")

packages/opencode/test/tool/read.test.ts

@@ -104,6 +104,21 @@ const asks = () => {
 }
 
 describe("tool.read external_directory permission", () => {
+  it.live("uses directory-relative read permission paths in non-git projects", () =>
+    Effect.gen(function* () {
+      const dir = yield* tmpdirScoped()
+      yield* put(path.join(dir, ".agents", "test.txt"), "hello world")
+
+      const { items, next } = asks()
+
+      const result = yield* exec(dir, { filePath: path.join(dir, ".agents", "test.txt") }, next)
+      expect(result.output).toContain("hello world")
+      const read = items.find((item) => item.permission === "read")
+      expect(read).toBeDefined()
+      expect(read!.patterns).toEqual([path.join(".agents", "test.txt")])
+    }),
+  )
+
   it.live("allows reading absolute path inside project directory", () =>
     Effect.gen(function* () {
       const dir = yield* tmpdirScoped()

packages/opencode/test/tool/write.test.ts

@@ -95,6 +95,32 @@ describe("tool.write", () => {
         }),
       ),
     )
+
+    it.live("uses directory-relative permission paths in non-git projects", () =>
+      provideTmpdirInstance((dir) =>
+        Effect.gen(function* () {
+          const filepath = path.join(dir, ".agents", "file.txt")
+          const calls: Array<{ patterns: readonly string[] }> = []
+
+          yield* run(
+            {
+              filePath: filepath,
+              content: "content",
+            },
+            {
+              ...ctx,
+              ask: (input) =>
+                Effect.sync(() => {
+                  calls.push({ patterns: input.patterns })
+                }),
+            },
+          )
+
+          expect(calls).toHaveLength(1)
+          expect(calls[0]?.patterns).toEqual([path.join(".agents", "file.txt")])
+        }),
+      ),
+    )
   })
 
   describe("existing file overwrite", () => {