refactor(agentic): write workspace files atomically

pkg/mcp/agentic/plan.go

@@ -483,7 +483,7 @@ func writePlan(dir string, plan *Plan) (string, error) {
 		return "", err
 	}
 
-	return path, coreio.Local.Write(path, string(data))
+	return path, writeAtomic(path, string(data))
 }
 
 func validPlanStatus(status string) bool {

pkg/mcp/agentic/prep.go

@@ -278,20 +278,20 @@ func (s *PrepSubsystem) prepWorkspace(ctx context.Context, _ *mcp.CallToolReques
 	// 2. Copy CLAUDE.md and GEMINI.md to workspace
 	claudeMdPath := filepath.Join(repoPath, "CLAUDE.md")
 	if data, err := coreio.Local.Read(claudeMdPath); err == nil {
-		coreio.Local.Write(filepath.Join(wsDir, "src", "CLAUDE.md"), data)
+		_ = writeAtomic(filepath.Join(wsDir, "src", "CLAUDE.md"), data)
 		out.ClaudeMd = true
 	}
 	// Copy GEMINI.md from core/agent (ethics framework for all agents)
 	agentGeminiMd := filepath.Join(s.codePath, "core", "agent", "GEMINI.md")
 	if data, err := coreio.Local.Read(agentGeminiMd); err == nil {
-		coreio.Local.Write(filepath.Join(wsDir, "src", "GEMINI.md"), data)
+		_ = writeAtomic(filepath.Join(wsDir, "src", "GEMINI.md"), data)
 	}
 
 	// Copy persona if specified
 	if persona != "" {
 		personaPath := filepath.Join(s.codePath, "core", "agent", "prompts", "personas", persona+".md")
 		if data, err := coreio.Local.Read(personaPath); err == nil {
-			coreio.Local.Write(filepath.Join(wsDir, "src", "PERSONA.md"), data)
+			_ = writeAtomic(filepath.Join(wsDir, "src", "PERSONA.md"), data)
 		}
 	}
 
@@ -301,7 +301,7 @@ func (s *PrepSubsystem) prepWorkspace(ctx context.Context, _ *mcp.CallToolReques
 	} else if input.Task != "" {
 		todo := fmt.Sprintf("# TASK: %s\n\n**Repo:** %s/%s\n**Status:** ready\n\n## Objective\n\n%s\n",
 			input.Task, input.Org, input.Repo, input.Task)
-		coreio.Local.Write(filepath.Join(wsDir, "src", "TODO.md"), todo)
+		_ = writeAtomic(filepath.Join(wsDir, "src", "TODO.md"), todo)
 	}
 
 	// 4. Generate CONTEXT.md from OpenBrain
@@ -434,7 +434,7 @@ Do NOT push. Commit only — a reviewer will verify and push.
 		prompt = "Read TODO.md and complete the task. Work in src/.\n"
 	}
 
-	coreio.Local.Write(filepath.Join(wsDir, "src", "PROMPT.md"), prompt)
+	_ = writeAtomic(filepath.Join(wsDir, "src", "PROMPT.md"), prompt)
 }
 
 // --- Plan template rendering ---
@@ -512,7 +512,7 @@ func (s *PrepSubsystem) writePlanFromTemplate(templateSlug string, variables map
 		plan.WriteString("\n**Commit after completing this phase.**\n\n---\n\n")
 	}
 
-	coreio.Local.Write(filepath.Join(wsDir, "src", "PLAN.md"), plan.String())
+	_ = writeAtomic(filepath.Join(wsDir, "src", "PLAN.md"), plan.String())
 }
 
 // --- Helpers (unchanged) ---
@@ -579,7 +579,7 @@ func (s *PrepSubsystem) pullWiki(ctx context.Context, org, repo, wsDir string) i
 			return '-'
 		}, page.Title) + ".md"
 
-		coreio.Local.Write(filepath.Join(wsDir, "src", "kb", filename), string(content))
+		_ = writeAtomic(filepath.Join(wsDir, "src", "kb", filename), string(content))
 		count++
 	}
 
@@ -593,7 +593,7 @@ func (s *PrepSubsystem) copySpecs(wsDir string) int {
 	for _, file := range specFiles {
 		src := filepath.Join(s.specsPath, file)
 		if data, err := coreio.Local.Read(src); err == nil {
-			coreio.Local.Write(filepath.Join(wsDir, "src", "specs", file), data)
+			_ = writeAtomic(filepath.Join(wsDir, "src", "specs", file), data)
 			count++
 		}
 	}
@@ -645,7 +645,7 @@ func (s *PrepSubsystem) generateContext(ctx context.Context, repo, wsDir string)
 		content.WriteString(fmt.Sprintf("### %d. %s [%s] (score: %.3f)\n\n%s\n\n", i+1, memProject, memType, score, memContent))
 	}
 
-	coreio.Local.Write(filepath.Join(wsDir, "src", "CONTEXT.md"), content.String())
+	_ = writeAtomic(filepath.Join(wsDir, "src", "CONTEXT.md"), content.String())
 	return len(result.Memories)
 }
 
@@ -682,7 +682,7 @@ func (s *PrepSubsystem) findConsumers(repo, wsDir string) int {
 			content += "- " + c + "\n"
 		}
 		content += fmt.Sprintf("\n**Breaking change risk: %d consumers.**\n", len(consumers))
-		coreio.Local.Write(filepath.Join(wsDir, "src", "CONSUMERS.md"), content)
+		_ = writeAtomic(filepath.Join(wsDir, "src", "CONSUMERS.md"), content)
 	}
 
 	return len(consumers)
@@ -699,7 +699,7 @@ func (s *PrepSubsystem) gitLog(repoPath, wsDir string) int {
 	lines := strings.Split(strings.TrimSpace(string(output)), "\n")
 	if len(lines) > 0 && lines[0] != "" {
 		content := "# Recent Changes\n\n```\n" + string(output) + "```\n"
-		coreio.Local.Write(filepath.Join(wsDir, "src", "RECENT.md"), content)
+		_ = writeAtomic(filepath.Join(wsDir, "src", "RECENT.md"), content)
 	}
 
 	return len(lines)
@@ -735,5 +735,5 @@ func (s *PrepSubsystem) generateTodo(ctx context.Context, org, repo string, issu
 	content += fmt.Sprintf("**Repo:** %s/%s\n\n---\n\n", org, repo)
 	content += "## Objective\n\n" + issueData.Body + "\n"
 
-	coreio.Local.Write(filepath.Join(wsDir, "src", "TODO.md"), content)
+	_ = writeAtomic(filepath.Join(wsDir, "src", "TODO.md"), content)
 }

pkg/mcp/agentic/resume.go

@@ -80,7 +80,7 @@ func (s *PrepSubsystem) resume(ctx context.Context, _ *mcp.CallToolRequest, inpu
 	if input.Answer != "" {
 		answerPath := filepath.Join(srcDir, "ANSWER.md")
 		content := fmt.Sprintf("# Answer\n\n%s\n", input.Answer)
-		if err := coreio.Local.Write(answerPath, content); err != nil {
+		if err := writeAtomic(answerPath, content); err != nil {
 			return nil, ResumeOutput{}, coreerr.E("resume", "failed to write ANSWER.md", err)
 		}
 	}

pkg/mcp/agentic/review_queue.go

@@ -236,7 +236,7 @@ func (s *PrepSubsystem) storeReviewOutput(repoDir, repo, reviewer, output string
 	}
 
 	name := fmt.Sprintf("%s-%s-%d.json", repo, reviewer, time.Now().Unix())
-	_ = coreio.Local.Write(filepath.Join(dataDir, name), string(data))
+	_ = writeAtomic(filepath.Join(dataDir, name), string(data))
 }
 
 func (s *PrepSubsystem) saveRateLimitState(info *RateLimitInfo) {
@@ -246,7 +246,7 @@ func (s *PrepSubsystem) saveRateLimitState(info *RateLimitInfo) {
 	if err != nil {
 		return
 	}
-	_ = coreio.Local.Write(path, string(data))
+	_ = writeAtomic(path, string(data))
 }
 
 func (s *PrepSubsystem) loadRateLimitState() *RateLimitInfo {

pkg/mcp/agentic/status.go

@@ -56,7 +56,7 @@ func writeStatus(wsDir string, status *WorkspaceStatus) error {
 	if err != nil {
 		return err
 	}
-	return coreio.Local.Write(filepath.Join(wsDir, "status.json"), string(data))
+	return writeAtomic(filepath.Join(wsDir, "status.json"), string(data))
 }
 
 func readStatus(wsDir string) (*WorkspaceStatus, error) {

pkg/mcp/agentic/write_atomic.go

@@ -0,0 +1,51 @@
+// SPDX-License-Identifier: EUPL-1.2
+
+package agentic
+
+import (
+	"os"
+	"path/filepath"
+
+	coreio "forge.lthn.ai/core/go-io"
+)
+
+// writeAtomic writes content to path by staging it in a temporary file and
+// renaming it into place.
+//
+// This avoids exposing partially written workspace files to agents that may
+// read status, prompt, or plan documents while they are being updated.
+func writeAtomic(path, content string) error {
+	dir := filepath.Dir(path)
+	if err := coreio.Local.EnsureDir(dir); err != nil {
+		return err
+	}
+
+	tmp, err := os.CreateTemp(dir, "."+filepath.Base(path)+".*.tmp")
+	if err != nil {
+		return err
+	}
+	tmpPath := tmp.Name()
+
+	cleanup := func() {
+		_ = tmp.Close()
+		_ = os.Remove(tmpPath)
+	}
+
+	if _, err := tmp.WriteString(content); err != nil {
+		cleanup()
+		return err
+	}
+	if err := tmp.Sync(); err != nil {
+		cleanup()
+		return err
+	}
+	if err := tmp.Close(); err != nil {
+		_ = os.Remove(tmpPath)
+		return err
+	}
+	if err := os.Rename(tmpPath, path); err != nil {
+		_ = os.Remove(tmpPath)
+		return err
+	}
+	return nil
+}