diff --git a/packages/opencode/src/tool/apply_patch.ts b/packages/opencode/src/tool/apply_patch.ts
index f9201be8a7db..040ad84ae0de 100644
--- a/packages/opencode/src/tool/apply_patch.ts
+++ b/packages/opencode/src/tool/apply_patch.ts
@@ -12,6 +12,7 @@ import { LSP } from "@/lsp/lsp"
 import { FSUtil } from "@opencode-ai/core/fs-util"
 import DESCRIPTION from "./apply_patch.txt"
 import { FileSystem } from "@opencode-ai/core/filesystem"
+import { relative } from "./relative"
 import { Format } from "../format"
 import * as Bom from "@/util/bom"
 
@@ -193,7 +194,7 @@ 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(instance, change.movePath ?? change.filePath).replaceAll("\\", "/"),
         type: change.type,
         patch: change.diff,
         additions: change.additions,
@@ -202,7 +203,7 @@ 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(instance, c.filePath).replaceAll("\\", "/"))
       yield* ctx.ask({
         permission: "edit",
         patterns: relativePaths,
@@ -273,13 +274,13 @@ 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(instance, change.filePath).replaceAll("\\", "/")}`
         }
         if (change.type === "delete") {
-          return `D ${path.relative(instance.worktree, change.filePath).replaceAll("\\", "/")}`
+          return `D ${relative(instance, change.filePath).replaceAll("\\", "/")}`
         }
         const target = change.movePath ?? change.filePath
-        return `M ${path.relative(instance.worktree, target).replaceAll("\\", "/")}`
+        return `M ${relative(instance, target).replaceAll("\\", "/")}`
       })
       let output = `Success. Updated the following files:\n${summaryLines.join("\n")}`
 
@@ -288,7 +289,7 @@ export const ApplyPatchTool = Tool.define(
         const target = change.movePath ?? change.filePath
         const block = LSP.Diagnostic.report(target, diagnostics[FSUtil.normalizePath(target)] ?? [])
         if (!block) continue
-        const rel = path.relative(instance.worktree, target).replaceAll("\\", "/")
+        const rel = relative(instance, target).replaceAll("\\", "/")
         output += `\n\nLSP errors detected in ${rel}, please fix:\n${block}`
       }
 
diff --git a/packages/opencode/src/tool/edit.ts b/packages/opencode/src/tool/edit.ts
index a92e4720c0fc..35d695c67bec 100644
--- a/packages/opencode/src/tool/edit.ts
+++ b/packages/opencode/src/tool/edit.ts
@@ -17,6 +17,7 @@ import { InstanceState } from "@/effect/instance-state"
 import { Snapshot } from "@/snapshot"
 import { assertExternalDirectoryEffect } from "./external-directory"
 import { FSUtil } from "@opencode-ai/core/fs-util"
+import { relative } from "./relative"
 import * as Bom from "@/util/bom"
 
 function normalizeLineEndings(text: string): string {
@@ -81,6 +82,7 @@ export const EditTool = Tool.define(
             ? params.filePath
             : path.join(instance.directory, params.filePath)
           yield* assertExternalDirectoryEffect(ctx, filePath)
+          const rel = relative(instance, filePath)
 
           let diff = ""
           let contentOld = ""
@@ -101,7 +103,7 @@ 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,
@@ -144,7 +146,7 @@ export const EditTool = Tool.define(
               )
               yield* ctx.ask({
                 permission: "edit",
-                patterns: [path.relative(instance.worktree, filePath)],
+                patterns: [rel],
                 always: ["*"],
                 metadata: {
                   filepath: filePath,
@@ -206,7 +208,7 @@ export const EditTool = Tool.define(
               diff,
               filediff,
             },
-            title: `${path.relative(instance.worktree, filePath)}`,
+            title: rel,
             output,
           }
         }),
diff --git a/packages/opencode/src/tool/lsp.ts b/packages/opencode/src/tool/lsp.ts
index a605cea749d5..a9b23e084bfb 100644
--- a/packages/opencode/src/tool/lsp.ts
+++ b/packages/opencode/src/tool/lsp.ts
@@ -7,6 +7,7 @@ import { InstanceState } from "@/effect/instance-state"
 import { pathToFileURL } from "url"
 import { assertExternalDirectoryEffect } from "./external-directory"
 import { FSUtil } from "@opencode-ai/core/fs-util"
+import { relative } from "./relative"
 
 const operations = [
   "goToDefinition",
@@ -62,7 +63,7 @@ export const LspTool = Tool.define(
 
           const uri = pathToFileURL(file).href
           const position = { file, line: args.line - 1, character: args.character - 1 }
-          const relPath = path.relative(instance.worktree, file)
+          const relPath = relative(instance, file)
           const detail =
             args.operation === "workspaceSymbol"
               ? ""
diff --git a/packages/opencode/src/tool/read.ts b/packages/opencode/src/tool/read.ts
index 678ed4451048..e7e55ded38cd 100644
--- a/packages/opencode/src/tool/read.ts
+++ b/packages/opencode/src/tool/read.ts
@@ -8,6 +8,7 @@ import DESCRIPTION from "./read.txt"
 import { InstanceState } from "@/effect/instance-state"
 import { assertExternalDirectoryEffect } from "./external-directory"
 import { Instruction } from "../session/instruction"
+import { relative } from "./relative"
 import { isPdfAttachment, sniffAttachmentMime } from "@/util/media"
 
 const DEFAULT_READ_LIMIT = 2000
@@ -238,7 +239,7 @@ export const ReadTool = Tool.define<
       if (process.platform === "win32") {
         filepath = FSUtil.normalizePath(filepath)
       }
-      const title = path.relative(instance.worktree, filepath)
+      const rel = relative(instance,  filepath)
 
       const stat = yield* fs.stat(filepath).pipe(
         Effect.catchIf(
@@ -254,7 +255,7 @@ export const ReadTool = Tool.define<
 
       yield* ctx.ask({
         permission: "read",
-        patterns: [path.relative(instance.worktree, filepath)],
+        patterns: [rel],
         always: ["*"],
         metadata: {},
       })
@@ -270,7 +271,7 @@ export const ReadTool = Tool.define<
         const truncated = start + sliced.length < items.length
 
         return {
-          title,
+          title: rel,
           output: [
             `<path>${filepath}</path>`,
             `<type>directory</type>`,
@@ -307,7 +308,7 @@ export const ReadTool = Tool.define<
         const bytes = yield* fs.readFile(filepath)
         const msg = isPdfAttachment(mime) ? "PDF read successfully" : "Image read successfully"
         return {
-          title,
+          title: rel,
           output: msg,
           metadata: {
             preview: msg,
@@ -357,7 +358,7 @@ export const ReadTool = Tool.define<
       }
 
       return {
-        title,
+        title: rel,
         output,
         metadata: {
           preview: file.raw.slice(0, 20).join("\n"),
diff --git a/packages/opencode/src/tool/relative.ts b/packages/opencode/src/tool/relative.ts
new file mode 100644
index 000000000000..df484b52f997
--- /dev/null
+++ b/packages/opencode/src/tool/relative.ts
@@ -0,0 +1,8 @@
+import path from "path"
+import type { InstanceContext } from "@/project/instance-context"
+
+export function relative(instance: InstanceContext, file: string) {
+
+  const root = instance.worktree === "/" ? instance.directory : instance.worktree
+  return path.relative(root, file)
+}
diff --git a/packages/opencode/src/tool/write.ts b/packages/opencode/src/tool/write.ts
index 37be6d8c47bc..0dccad816505 100644
--- a/packages/opencode/src/tool/write.ts
+++ b/packages/opencode/src/tool/write.ts
@@ -13,6 +13,7 @@ import { FSUtil } from "@opencode-ai/core/fs-util"
 import { InstanceState } from "@/effect/instance-state"
 import { trimDiff } from "./edit"
 import { assertExternalDirectoryEffect } from "./external-directory"
+import { relative } from "./relative"
 import * as Bom from "@/util/bom"
 
 const MAX_PROJECT_DIAGNOSTICS_FILES = 5
@@ -49,11 +50,13 @@ export const WriteTool = Tool.define(
           const desiredBom = source.bom || next.bom
           const contentOld = source.text
           const contentNew = next.text
+          
+          const rel = relative(instance, filepath)
 
           const diff = trimDiff(createTwoFilesPatch(filepath, filepath, contentOld, contentNew))
           yield* ctx.ask({
             permission: "edit",
-            patterns: [path.relative(instance.worktree, filepath)],
+            patterns: [rel],
             always: ["*"],
             metadata: {
               filepath,
@@ -90,7 +93,7 @@ export const WriteTool = Tool.define(
           }
 
           return {
-            title: path.relative(instance.worktree, filepath),
+            title: rel,
             metadata: {
               diagnostics,
               filepath,
diff --git a/packages/opencode/test/tool/apply_patch.test.ts b/packages/opencode/test/tool/apply_patch.test.ts
index 01a09add8732..ec8f8109c11b 100644
--- a/packages/opencode/test/tool/apply_patch.test.ts
+++ b/packages/opencode/test/tool/apply_patch.test.ts
@@ -188,6 +188,20 @@ describe("tool.apply_patch freeform", () => {
     { git: true },
   )
 
+  it.instance("uses directory-relative permission paths in non-git projects", () =>
+    Effect.gen(function* () {
+      const { ctx, calls } = makeCtx()
+
+      const patchText = "*** Begin Patch\n*** Add File: .agents/new.txt\n+created\n*** End Patch"
+
+      yield* 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")
+    }),
+  )
+
   it.instance("applies multiple hunks to one file", () =>
     Effect.gen(function* () {
       const test = yield* TestInstance
diff --git a/packages/opencode/test/tool/edit.test.ts b/packages/opencode/test/tool/edit.test.ts
index 12db53551856..23bf63d05176 100644
--- a/packages/opencode/test/tool/edit.test.ts
+++ b/packages/opencode/test/tool/edit.test.ts
@@ -143,6 +143,28 @@ describe("tool.edit", () => {
         yield* Deferred.await(updated)
       }),
     )
+
+    it.instance("uses directory-relative permission paths in non-git projects", () =>
+      Effect.gen(function* () {
+        const test = yield* TestInstance
+        const filepath = path.join(test.directory, ".agents", "file.txt")
+        const calls: Array<{ patterns: readonly string[] }> = []
+
+        yield* run(
+          { 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")])
+      }),
+    )
   })
 
   describe("editing existing files", () => {
diff --git a/packages/opencode/test/tool/read.test.ts b/packages/opencode/test/tool/read.test.ts
index 67205f56e384..88b4cac13ab3 100644
--- a/packages/opencode/test/tool/read.test.ts
+++ b/packages/opencode/test/tool/read.test.ts
@@ -146,6 +146,21 @@ 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()
diff --git a/packages/opencode/test/tool/write.test.ts b/packages/opencode/test/tool/write.test.ts
index 63a2a52aa986..bbe50073ad8d 100644
--- a/packages/opencode/test/tool/write.test.ts
+++ b/packages/opencode/test/tool/write.test.ts
@@ -91,6 +91,31 @@ describe("tool.write", () => {
         expect(content).toBe("relative content")
       }),
     )
+
+    it.instance("uses directory-relative permission paths in non-git projects", () =>
+      Effect.gen(function* () {
+        const test = yield* TestInstance
+        const filepath = path.join(test.directory, ".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", () => {