fix(athena): resolve task output files to project directory instead of process.cwd()

task-output-writer wrote to process.cwd()/.sisyphus/task-outputs/ while
council_finalize read from ctx.directory/.sisyphus/task-outputs/. When
these differ, all output files appear missing.

Fix by passing directory to writeTaskOutput from BackgroundManager, and
adding basePath to council_read. Also removes process.chdir() from tests
that was masking the bug.

src/features/background-agent/manager.ts

@@ -1709,7 +1709,7 @@ export class BackgroundManager {
 
     // Write output to file if requested (before status flip)
     if (task.writeOutputToFile) {
-      const filePath = await writeTaskOutput(task, this.client)
+      const filePath = await writeTaskOutput(task, this.client, this.directory)
       if (filePath) task.outputFilePath = filePath
     }
 

src/features/background-agent/task-output-writer.test.ts

@@ -74,7 +74,7 @@ describe("writeTaskOutput", () => {
       ])
       const task = createMockTask()
 
-      const result = await writeTaskOutput(task, client)
+      const result = await writeTaskOutput(task, client, ".")
 
       expect(result).toBe(`${TEST_OUTPUT_DIR}/bg_test_123.md`)
       expect(existsSync(result!)).toBe(true)
@@ -99,7 +99,7 @@ describe("writeTaskOutput", () => {
       const client = createMockClient([])
       const task = createMockTask({ sessionID: undefined })
 
-      const result = await writeTaskOutput(task, client)
+      const result = await writeTaskOutput(task, client, ".")
 
       expect(result).toBeNull()
       expect(existsSync(`${TEST_OUTPUT_DIR}/bg_test_123.md`)).toBe(false)
@@ -111,7 +111,7 @@ describe("writeTaskOutput", () => {
       const client = createErrorClient("Session not found")
       const task = createMockTask()
 
-      const result = await writeTaskOutput(task, client)
+      const result = await writeTaskOutput(task, client, ".")
 
       expect(result).toBeNull()
       expect(existsSync(`${TEST_OUTPUT_DIR}/bg_test_123.md`)).toBe(false)
@@ -123,7 +123,7 @@ describe("writeTaskOutput", () => {
       const client = createMockClient([])
       const task = createMockTask()
 
-      const result = await writeTaskOutput(task, client)
+      const result = await writeTaskOutput(task, client, ".")
 
       expect(result).toBe(`${TEST_OUTPUT_DIR}/bg_test_123.md`)
       expect(existsSync(result!)).toBe(true)
@@ -149,7 +149,7 @@ describe("writeTaskOutput", () => {
       ])
       const task = createMockTask()
 
-      const result = await writeTaskOutput(task, client)
+      const result = await writeTaskOutput(task, client, ".")
 
       expect(result).toBe(`${TEST_OUTPUT_DIR}/bg_test_123.md`)
       expect(existsSync(TEST_OUTPUT_DIR)).toBe(true)
@@ -171,7 +171,7 @@ describe("writeTaskOutput", () => {
       ])
       const task = createMockTask()
 
-      const result = await writeTaskOutput(task, client)
+      const result = await writeTaskOutput(task, client, ".")
 
       const content = await readFile(result!, "utf-8")
       expect(content).toContain("Let me think about this...")
@@ -195,7 +195,7 @@ describe("writeTaskOutput", () => {
       ])
       const task = createMockTask()
 
-      const result = await writeTaskOutput(task, client)
+      const result = await writeTaskOutput(task, client, ".")
 
       const content = await readFile(result!, "utf-8")
       const firstIdx = content.indexOf("First message")
@@ -209,7 +209,7 @@ describe("writeTaskOutput", () => {
       const client = createMockClient([])
       const task = createMockTask({ completedAt: undefined })
 
-      const result = await writeTaskOutput(task, client)
+      const result = await writeTaskOutput(task, client, ".")
 
       const content = await readFile(result!, "utf-8")
       expect(content).toContain("completed_at: unknown")

src/features/background-agent/task-output-writer.ts

@@ -1,5 +1,5 @@
 import { mkdir, writeFile, rename } from "node:fs/promises"
-import { dirname } from "node:path"
+import { dirname, join } from "node:path"
 import { log } from "../../shared"
 import type { BackgroundTask } from "./types"
 import type { BackgroundOutputClient } from "../../tools/background-task/clients"
@@ -53,6 +53,7 @@ function formatTranscript(
 export async function writeTaskOutput(
   task: BackgroundTask,
   client: BackgroundOutputClient,
+  directory: string,
 ): Promise<string | null> {
   if (!task.sessionID) {
     return null
@@ -74,7 +75,7 @@ export async function writeTaskOutput(
     const transcript = formatTranscript(messages)
     const content = `${frontmatter}\n\n${transcript}`
 
-    const outputPath = `${OUTPUT_DIR}/${task.id}.md`
+    const outputPath = join(directory, OUTPUT_DIR, `${task.id}.md`)
     const tmpPath = `${outputPath}.tmp`
 
     await mkdir(dirname(outputPath), { recursive: true })

src/plugin/tool-registry.ts

@@ -282,7 +282,7 @@ export function createToolRegistry(args: {
     ...hashlineToolsRecord,
     prepare_council_prompt: createPrepareCouncilPromptTool(ctx.directory),
     council_finalize: createCouncilFinalize(ctx.directory),
-    council_read: createCouncilRead(),
+    council_read: createCouncilRead(ctx.directory),
   }
 
   for (const toolDefinition of Object.values(allTools)) {

src/tools/council-archive/council-flow.integration.test.ts

@@ -75,16 +75,13 @@ function createMockManager(tasks: Record<string, Partial<BackgroundTask>>): Back
 }
 
 let tmpDir: string
-let originalCwd: string
 
 beforeEach(async () => {
   tmpDir = await mkdtemp(join(tmpdir(), "council-flow-"))
   await mkdir(join(tmpDir, ".sisyphus", "task-outputs"), { recursive: true })
-  originalCwd = process.cwd()
 })
 
 afterEach(async () => {
-  process.chdir(originalCwd)
   await rm(tmpDir, { recursive: true, force: true })
 })
 
@@ -142,8 +139,7 @@ describe("council archive integration flow", () => {
           expect(archiveContent).toBe(agents[i].response)
         }
 
-        process.chdir(tmpDir)
+        const readTool = createCouncilRead(tmpDir)
-        const readTool = createCouncilRead()
 
         for (let i = 0; i < agents.length; i++) {
           const taskOutputPath = join(".sisyphus", "task-outputs", `${agents[i].id}.md`)
@@ -183,8 +179,7 @@ describe("council archive integration flow", () => {
         const archiveContent = await readFile(join(tmpDir, member.archive_file!), "utf-8")
         expect(archiveContent).toBe("Analysis still in progress...")
 
-        process.chdir(tmpDir)
+        const readTool = createCouncilRead(tmpDir)
-        const readTool = createCouncilRead()
         const taskOutputPath = join(".sisyphus", "task-outputs", `${taskId}.md`)
         const readResult = await readTool.execute({ file_path: taskOutputPath }, toolContext)
         const parsed = JSON.parse(readResult)
@@ -284,8 +279,7 @@ describe("council archive integration flow", () => {
         const fullContent = await readFile(join(tmpDir, member.archive_file!), "utf-8")
         expect(fullContent).toHaveLength(9000)
 
-        process.chdir(tmpDir)
+        const readTool = createCouncilRead(tmpDir)
-        const readTool = createCouncilRead()
         const taskOutputPath = join(".sisyphus", "task-outputs", `${taskId}.md`)
         const readResult = await readTool.execute({ file_path: taskOutputPath }, toolContext)
         const parsed = JSON.parse(readResult)

src/tools/council-archive/create-council-read.test.ts

@@ -32,10 +32,9 @@ describe("createCouncilRead", () => {
       const archivePath = join(sisyphusDir, "member-1.txt")
       await writeFile(archivePath, "Some preamble\n<COUNCIL_MEMBER_RESPONSE>Full analysis here</COUNCIL_MEMBER_RESPONSE>")
 
-      const tool = createCouncilRead()
+      const tool = createCouncilRead(tempDir)
       const relativePath = `.sisyphus/member-1.txt`
 
-      process.chdir(tempDir)
       const result = await tool.execute({ file_path: relativePath }, toolContext)
       const parsed = JSON.parse(result)
 
@@ -50,10 +49,9 @@ describe("createCouncilRead", () => {
       const archivePath = join(sisyphusDir, "member-2.txt")
       await writeFile(archivePath, "<COUNCIL_MEMBER_RESPONSE>Partial analysis still writing...")
 
-      const tool = createCouncilRead()
+      const tool = createCouncilRead(tempDir)
       const relativePath = `.sisyphus/member-2.txt`
 
-      process.chdir(tempDir)
       const result = await tool.execute({ file_path: relativePath }, toolContext)
       const parsed = JSON.parse(result)
 
@@ -67,10 +65,9 @@ describe("createCouncilRead", () => {
       const archivePath = join(sisyphusDir, "member-3.txt")
       await writeFile(archivePath, "Just some plain text without any tags.")
 
-      const tool = createCouncilRead()
+      const tool = createCouncilRead(tempDir)
       const relativePath = `.sisyphus/member-3.txt`
 
-      process.chdir(tempDir)
       const result = await tool.execute({ file_path: relativePath }, toolContext)
       const parsed = JSON.parse(result)
 
@@ -80,7 +77,7 @@ describe("createCouncilRead", () => {
 
   describe("#given a path outside .sisyphus/", () => {
     it("#then returns Access denied error", async () => {
-      const tool = createCouncilRead()
+      const tool = createCouncilRead(tempDir)
       const result = await tool.execute({ file_path: "/etc/passwd" }, toolContext)
       const parsed = JSON.parse(result)
 
@@ -90,10 +87,9 @@ describe("createCouncilRead", () => {
 
   describe("#given a missing file within .sisyphus/", () => {
     it("#then returns has_response false with File not found error", async () => {
-      const tool = createCouncilRead()
+      const tool = createCouncilRead(tempDir)
       const relativePath = `.sisyphus/nonexistent-file.txt`
 
-      process.chdir(tempDir)
       const result = await tool.execute({ file_path: relativePath }, toolContext)
       const parsed = JSON.parse(result)
 
@@ -105,7 +101,7 @@ describe("createCouncilRead", () => {
 
   describe("#given a path traversal attempt", () => {
     it("#then returns Access denied error", async () => {
-      const tool = createCouncilRead()
+      const tool = createCouncilRead(tempDir)
       const result = await tool.execute({ file_path: "../../../etc/passwd" }, toolContext)
       const parsed = JSON.parse(result)
 

src/tools/council-archive/create-council-read.ts

@@ -1,8 +1,9 @@
 import { tool, type ToolDefinition } from "@opencode-ai/plugin"
 import { readFile } from "node:fs/promises"
+import { join } from "node:path"
 import { extractCouncilResponse } from "./council-response-extractor"
 
-export function createCouncilRead(): ToolDefinition {
+export function createCouncilRead(basePath?: string): ToolDefinition {
   return tool({
     description:
       "Read a council archive file and extract the council member response. Use this to access full results for truncated members or for follow-up/cross-check analysis.",
@@ -15,7 +16,9 @@ export function createCouncilRead(): ToolDefinition {
       }
 
       try {
-        const content = await readFile(args.file_path, "utf-8")
+        const base = basePath ?? process.cwd()
+        const absPath = join(base, args.file_path)
+        const content = await readFile(absPath, "utf-8")
         const extraction = extractCouncilResponse(content)
         return JSON.stringify(extraction, null, 2)
       } catch {