Merge remote-tracking branch 'public-gh/master' into paperclip-routines

* public-gh/master: (46 commits)
  chore(lockfile): refresh pnpm-lock.yaml (#1377)
  fix: manage codex home per company by default
  Ensure agent home directories exist before use
  Handle directory entries in imported zip archives
  Fix portability import and org chart test blockers
  Fix PR verify failures after merge
  fix: address greptile follow-up feedback
  Address remaining Greptile portability feedback
  docs: clarify quickstart npx usage
  Add guarded dev restart handling
  Fix PAP-576 settings toggles and transcript default
  Add username log censor setting
  fix: use standard toggle component for permission controls
  fix: add missing setPrincipalPermission mock in portability tests
  fix: use fixed 1280x640 dimensions for org chart export image
  Adjust default CEO onboarding task copy
  fix: link Agent Company to agentcompanies.io in export README
  fix: strip agents and projects sections from COMPANY.md export body
  fix: default company export page to README.md instead of first file
  Add default agent instructions bundle
  ...

# Conflicts:
#	packages/adapters/pi-local/src/server/execute.ts
#	packages/db/src/migrations/meta/0039_snapshot.json
#	packages/db/src/migrations/meta/_journal.json
#	server/src/__tests__/agent-permissions-routes.test.ts
#	server/src/__tests__/agent-skills-routes.test.ts
#	server/src/services/company-portability.ts
#	skills/paperclip/references/company-skills.md
#	ui/src/api/agents.ts

packages/adapters/codex-local/src/index.ts

@@ -41,6 +41,7 @@ Operational fields:
 Notes:
 - Prompts are piped via stdin (Codex receives "-" prompt argument).
 - Paperclip injects desired local skills into the active workspace's ".agents/skills" directory at execution time so Codex can discover "$paperclip" and related skills without coupling them to the user's login home.
+- Unless explicitly overridden in adapter config, Paperclip runs Codex with a per-company managed CODEX_HOME under the active Paperclip instance and seeds auth/config from the shared Codex home (the CODEX_HOME env var, when set, or ~/.codex).
 - Some model/tool combinations reject certain effort levels (for example minimal with web search enabled).
 - When Paperclip realizes a workspace/runtime for a run, it injects PAPERCLIP_WORKSPACE_* and PAPERCLIP_RUNTIME_* env vars for agent-side tooling.
 `;

packages/adapters/codex-local/src/server/codex-home.ts

@@ -6,6 +6,7 @@ import type { AdapterExecutionContext } from "@paperclipai/adapter-utils";
 const TRUTHY_ENV_RE = /^(1|true|yes|on)$/i;
 const COPIED_SHARED_FILES = ["config.json", "config.toml", "instructions.md"] as const;
 const SYMLINKED_SHARED_FILES = ["auth.json"] as const;
+const DEFAULT_PAPERCLIP_INSTANCE_ID = "default";
 
 function nonEmpty(value: string | undefined): string | null {
   return typeof value === "string" && value.trim().length > 0 ? value.trim() : null;
@@ -15,35 +16,26 @@ export async function pathExists(candidate: string): Promise<boolean> {
   return fs.access(candidate).then(() => true).catch(() => false);
 }
 
-export function resolveCodexHomeDir(
+export function resolveSharedCodexHomeDir(
   env: NodeJS.ProcessEnv = process.env,
-  companyId?: string,
 ): string {
   const fromEnv = nonEmpty(env.CODEX_HOME);
-  const baseHome = fromEnv ? path.resolve(fromEnv) : path.join(os.homedir(), ".codex");
-  return companyId ? path.join(baseHome, "companies", companyId) : baseHome;
+  return fromEnv ? path.resolve(fromEnv) : path.join(os.homedir(), ".codex");
 }
 
 function isWorktreeMode(env: NodeJS.ProcessEnv): boolean {
   return TRUTHY_ENV_RE.test(env.PAPERCLIP_IN_WORKTREE ?? "");
 }
 
-function resolveWorktreeCodexHomeDir(
+export function resolveManagedCodexHomeDir(
   env: NodeJS.ProcessEnv,
   companyId?: string,
-): string | null {
-  if (!isWorktreeMode(env)) return null;
-  const paperclipHome = nonEmpty(env.PAPERCLIP_HOME);
-  if (!paperclipHome) return null;
-  const instanceId = nonEmpty(env.PAPERCLIP_INSTANCE_ID);
-  if (instanceId) {
-    return companyId
-      ? path.resolve(paperclipHome, "instances", instanceId, "companies", companyId, "codex-home")
-      : path.resolve(paperclipHome, "instances", instanceId, "codex-home");
-  }
+): string {
+  const paperclipHome = nonEmpty(env.PAPERCLIP_HOME) ?? path.resolve(os.homedir(), ".paperclip");
+  const instanceId = nonEmpty(env.PAPERCLIP_INSTANCE_ID) ?? DEFAULT_PAPERCLIP_INSTANCE_ID;
   return companyId
-    ? path.resolve(paperclipHome, "companies", companyId, "codex-home")
-    : path.resolve(paperclipHome, "codex-home");
+    ? path.resolve(paperclipHome, "instances", instanceId, "companies", companyId, "codex-home")
+    : path.resolve(paperclipHome, "instances", instanceId, "codex-home");
 }
 
 async function ensureParentDir(target: string): Promise<void> {
@@ -79,15 +71,14 @@ async function ensureCopiedFile(target: string, source: string): Promise<void> {
   await fs.copyFile(source, target);
 }
 
-export async function prepareWorktreeCodexHome(
+export async function prepareManagedCodexHome(
   env: NodeJS.ProcessEnv,
   onLog: AdapterExecutionContext["onLog"],
   companyId?: string,
-): Promise<string | null> {
-  const targetHome = resolveWorktreeCodexHomeDir(env, companyId);
-  if (!targetHome) return null;
+): Promise<string> {
+  const targetHome = resolveManagedCodexHomeDir(env, companyId);
 
-  const sourceHome = resolveCodexHomeDir(env);
+  const sourceHome = resolveSharedCodexHomeDir(env);
   if (path.resolve(sourceHome) === path.resolve(targetHome)) return targetHome;
 
   await fs.mkdir(targetHome, { recursive: true });
@@ -106,7 +97,7 @@ export async function prepareWorktreeCodexHome(
 
   await onLog(
     "stdout",
-    `[paperclip] Using worktree-isolated Codex home "${targetHome}" (seeded from "${sourceHome}").\n`,
+    `[paperclip] Using ${isWorktreeMode(env) ? "worktree-isolated" : "Paperclip-managed"} Codex home "${targetHome}" (seeded from "${sourceHome}").\n`,
   );
   return targetHome;
 }

packages/adapters/codex-local/src/server/execute.ts

@@ -21,7 +21,7 @@ import {
   runChildProcess,
 } from "@paperclipai/adapter-utils/server-utils";
 import { parseCodexJsonl, isCodexUnknownSessionError } from "./parse.js";
-import { pathExists, prepareWorktreeCodexHome, resolveCodexHomeDir } from "./codex-home.js";
+import { pathExists, prepareManagedCodexHome, resolveManagedCodexHomeDir } from "./codex-home.js";
 import { resolveCodexDesiredSkillNames } from "./skills.js";
 
 const __moduleDir = path.dirname(fileURLToPath(import.meta.url));
@@ -268,10 +268,11 @@ export async function execute(ctx: AdapterExecutionContext): Promise<AdapterExec
   const codexSkillEntries = await readPaperclipRuntimeSkillEntries(config, __moduleDir);
   const desiredSkillNames = resolveCodexDesiredSkillNames(config, codexSkillEntries);
   await ensureAbsoluteDirectory(cwd, { createIfMissing: true });
-  const preparedWorktreeCodexHome =
-    configuredCodexHome ? null : await prepareWorktreeCodexHome(process.env, onLog, agent.companyId);
-  const defaultCodexHome = resolveCodexHomeDir(process.env, agent.companyId);
-  const effectiveCodexHome = configuredCodexHome ?? preparedWorktreeCodexHome ?? defaultCodexHome;
+  const preparedManagedCodexHome =
+    configuredCodexHome ? null : await prepareManagedCodexHome(process.env, onLog, agent.companyId);
+  const defaultCodexHome = resolveManagedCodexHomeDir(process.env, agent.companyId);
+  const effectiveCodexHome = configuredCodexHome ?? preparedManagedCodexHome ?? defaultCodexHome;
+  await fs.mkdir(effectiveCodexHome, { recursive: true });
   const codexWorkspaceSkillsDir = resolveCodexWorkspaceSkillsDir(cwd);
   await ensureCodexSkillsInjected(
     onLog,

packages/adapters/codex-local/src/ui/parse-stdout.ts

@@ -1,8 +1,4 @@
-import {
-  redactHomePathUserSegments,
-  redactHomePathUserSegmentsInValue,
-  type TranscriptEntry,
-} from "@paperclipai/adapter-utils";
+import { type TranscriptEntry } from "@paperclipai/adapter-utils";
 
 function safeJsonParse(text: string): unknown {
   try {
@@ -43,12 +39,12 @@ function errorText(value: unknown): string {
 }
 
 function stringifyUnknown(value: unknown): string {
-  if (typeof value === "string") return redactHomePathUserSegments(value);
+  if (typeof value === "string") return value;
   if (value === null || value === undefined) return "";
   try {
-    return JSON.stringify(redactHomePathUserSegmentsInValue(value), null, 2);
+    return JSON.stringify(value, null, 2);
   } catch {
-    return redactHomePathUserSegments(String(value));
+    return String(value);
   }
 }
 
@@ -61,8 +57,8 @@ function parseCommandExecutionItem(
   const command = asString(item.command);
   const status = asString(item.status);
   const exitCode = typeof item.exit_code === "number" && Number.isFinite(item.exit_code) ? item.exit_code : null;
-  const safeCommand = redactHomePathUserSegments(command);
-  const output = redactHomePathUserSegments(asString(item.aggregated_output)).replace(/\s+$/, "");
+  const safeCommand = command;
+  const output = asString(item.aggregated_output).replace(/\s+$/, "");
 
   if (phase === "started") {
     return [{
@@ -109,7 +105,7 @@ function parseFileChangeItem(item: Record<string, unknown>, ts: string): Transcr
     .filter((change): change is Record<string, unknown> => Boolean(change))
     .map((change) => {
       const kind = asString(change.kind, "update");
-      const path = redactHomePathUserSegments(asString(change.path, "unknown"));
+      const path = asString(change.path, "unknown");
       return `${kind} ${path}`;
     });
 
@@ -131,13 +127,13 @@ function parseCodexItem(
 
   if (itemType === "agent_message") {
     const text = asString(item.text);
-    if (text) return [{ kind: "assistant", ts, text: redactHomePathUserSegments(text) }];
+    if (text) return [{ kind: "assistant", ts, text }];
     return [];
   }
 
   if (itemType === "reasoning") {
     const text = asString(item.text);
-    if (text) return [{ kind: "thinking", ts, text: redactHomePathUserSegments(text) }];
+    if (text) return [{ kind: "thinking", ts, text }];
     return [{ kind: "system", ts, text: phase === "started" ? "reasoning started" : "reasoning completed" }];
   }
 
@@ -153,9 +149,9 @@ function parseCodexItem(
     return [{
       kind: "tool_call",
       ts,
-      name: redactHomePathUserSegments(asString(item.name, "unknown")),
+      name: asString(item.name, "unknown"),
       toolUseId: asString(item.id),
-      input: redactHomePathUserSegmentsInValue(item.input ?? {}),
+      input: item.input ?? {},
     }];
   }
 
@@ -167,12 +163,12 @@ function parseCodexItem(
       asString(item.result) ||
       stringifyUnknown(item.content ?? item.output ?? item.result);
     const isError = item.is_error === true || asString(item.status) === "error";
-    return [{ kind: "tool_result", ts, toolUseId, content: redactHomePathUserSegments(content), isError }];
+    return [{ kind: "tool_result", ts, toolUseId, content, isError }];
   }
 
   if (itemType === "error" && phase === "completed") {
     const text = errorText(item.message ?? item.error ?? item);
-    return [{ kind: "stderr", ts, text: redactHomePathUserSegments(text || "error") }];
+    return [{ kind: "stderr", ts, text: text || "error" }];
   }
 
   const id = asString(item.id);
@@ -181,14 +177,14 @@ function parseCodexItem(
   return [{
     kind: "system",
     ts,
-    text: redactHomePathUserSegments(`item ${phase}: ${itemType || "unknown"}${meta ? ` (${meta})` : ""}`),
+    text: `item ${phase}: ${itemType || "unknown"}${meta ? ` (${meta})` : ""}`,
   }];
 }
 
 export function parseCodexStdoutLine(line: string, ts: string): TranscriptEntry[] {
   const parsed = asRecord(safeJsonParse(line));
   if (!parsed) {
-    return [{ kind: "stdout", ts, text: redactHomePathUserSegments(line) }];
+    return [{ kind: "stdout", ts, text: line }];
   }
 
   const type = asString(parsed.type);
@@ -198,8 +194,8 @@ export function parseCodexStdoutLine(line: string, ts: string): TranscriptEntry[
     return [{
       kind: "init",
       ts,
-      model: redactHomePathUserSegments(asString(parsed.model, "codex")),
-      sessionId: redactHomePathUserSegments(threadId),
+      model: asString(parsed.model, "codex"),
+      sessionId: threadId,
     }];
   }
 
@@ -221,15 +217,15 @@ export function parseCodexStdoutLine(line: string, ts: string): TranscriptEntry[
     return [{
       kind: "result",
       ts,
-      text: redactHomePathUserSegments(asString(parsed.result)),
+      text: asString(parsed.result),
       inputTokens,
       outputTokens,
       cachedTokens,
       costUsd: asNumber(parsed.total_cost_usd),
-      subtype: redactHomePathUserSegments(asString(parsed.subtype)),
+      subtype: asString(parsed.subtype),
       isError: parsed.is_error === true,
       errors: Array.isArray(parsed.errors)
-        ? parsed.errors.map(errorText).map(redactHomePathUserSegments).filter(Boolean)
+        ? parsed.errors.map(errorText).filter(Boolean)
         : [],
     }];
   }
@@ -243,21 +239,21 @@ export function parseCodexStdoutLine(line: string, ts: string): TranscriptEntry[
     return [{
       kind: "result",
       ts,
-      text: redactHomePathUserSegments(asString(parsed.result)),
+      text: asString(parsed.result),
       inputTokens,
       outputTokens,
       cachedTokens,
       costUsd: asNumber(parsed.total_cost_usd),
-      subtype: redactHomePathUserSegments(asString(parsed.subtype, "turn.failed")),
+      subtype: asString(parsed.subtype, "turn.failed"),
       isError: true,
-      errors: message ? [redactHomePathUserSegments(message)] : [],
+      errors: message ? [message] : [],
     }];
   }
 
   if (type === "error") {
     const message = errorText(parsed.message ?? parsed.error ?? parsed);
-    return [{ kind: "stderr", ts, text: redactHomePathUserSegments(message || line) }];
+    return [{ kind: "stderr", ts, text: message || line }];
   }
 
-  return [{ kind: "stdout", ts, text: redactHomePathUserSegments(line) }];
+  return [{ kind: "stdout", ts, text: line }];
 }

packages/adapters/pi-local/src/server/execute.ts

@@ -80,12 +80,12 @@ async function ensurePiSkillsInjected(
       if (result === "skipped") continue;
       await onLog(
         "stderr",
-        `[paperclip] ${result === "repaired" ? "Repaired" : "Injected"} Pi skill "${entry.key}" into ${PI_AGENT_SKILLS_DIR}\n`,
+        `[paperclip] ${result === "repaired" ? "Repaired" : "Injected"} Pi skill "${entry.runtimeName}" into ${PI_AGENT_SKILLS_DIR}\n`,
       );
     } catch (err) {
       await onLog(
         "stderr",
-        `[paperclip] Failed to inject Pi skill "${entry.key}" into ${PI_AGENT_SKILLS_DIR}: ${err instanceof Error ? err.message : String(err)}\n`,
+        `[paperclip] Failed to inject Pi skill "${entry.runtimeName}" into ${PI_AGENT_SKILLS_DIR}: ${err instanceof Error ? err.message : String(err)}\n`,
       );
     }
   }