fix: align embedded postgres ctor types with initdbFlags usage

docs: consolidate dated plan docs and naming guidance

AGENTS.md

@@ -78,6 +78,9 @@ If you change schema/API behavior, update all impacted layers:
 4. Do not replace strategic docs wholesale unless asked.
 Prefer additive updates. Keep `doc/SPEC.md` and `doc/SPEC-implementation.md` aligned.
 
+5. Keep plan docs dated and centralized.
+New plan documents belong in `doc/plans/` and should use `YYYY-MM-DD-slug.md` filenames.
+
 ## 6. Database Change Workflow
 
 When changing data model:

cli/src/commands/client/agent.ts

@@ -1,5 +1,9 @@
 import { Command } from "commander";
 import type { Agent } from "@paperclipai/shared";
+import {
+  removeMaintainerOnlySkillSymlinks,
+  resolvePaperclipSkillsDir,
+} from "@paperclipai/adapter-utils/server-utils";
 import fs from "node:fs/promises";
 import os from "node:os";
 import path from "node:path";
@@ -34,15 +38,12 @@ interface SkillsInstallSummary {
   tool: "codex" | "claude";
   target: string;
   linked: string[];
+  removed: string[];
   skipped: string[];
   failed: Array<{ name: string; error: string }>;
 }
 
 const __moduleDir = path.dirname(fileURLToPath(import.meta.url));
-const PAPERCLIP_SKILLS_CANDIDATES = [
-  path.resolve(__moduleDir, "../../../../../skills"), // dev: cli/src/commands/client -> repo root/skills
-  path.resolve(process.cwd(), "skills"),
-];
 
 function codexSkillsHome(): string {
   const fromEnv = process.env.CODEX_HOME?.trim();
@@ -56,14 +57,6 @@ function claudeSkillsHome(): string {
   return path.join(base, "skills");
 }
 
-async function resolvePaperclipSkillsDir(): Promise<string | null> {
-  for (const candidate of PAPERCLIP_SKILLS_CANDIDATES) {
-    const isDir = await fs.stat(candidate).then((s) => s.isDirectory()).catch(() => false);
-    if (isDir) return candidate;
-  }
-  return null;
-}
-
 async function installSkillsForTarget(
   sourceSkillsDir: string,
   targetSkillsDir: string,
@@ -73,20 +66,65 @@ async function installSkillsForTarget(
     tool,
     target: targetSkillsDir,
     linked: [],
+    removed: [],
     skipped: [],
     failed: [],
   };
 
   await fs.mkdir(targetSkillsDir, { recursive: true });
   const entries = await fs.readdir(sourceSkillsDir, { withFileTypes: true });
+  summary.removed = await removeMaintainerOnlySkillSymlinks(
+    targetSkillsDir,
+    entries.filter((entry) => entry.isDirectory()).map((entry) => entry.name),
+  );
   for (const entry of entries) {
     if (!entry.isDirectory()) continue;
     const source = path.join(sourceSkillsDir, entry.name);
     const target = path.join(targetSkillsDir, entry.name);
     const existing = await fs.lstat(target).catch(() => null);
     if (existing) {
-      summary.skipped.push(entry.name);
-      continue;
+      if (existing.isSymbolicLink()) {
+        let linkedPath: string | null = null;
+        try {
+          linkedPath = await fs.readlink(target);
+        } catch (err) {
+          await fs.unlink(target);
+          try {
+            await fs.symlink(source, target);
+            summary.linked.push(entry.name);
+            continue;
+          } catch (linkErr) {
+            summary.failed.push({
+              name: entry.name,
+              error:
+                err instanceof Error && linkErr instanceof Error
+                  ? `${err.message}; then ${linkErr.message}`
+                  : err instanceof Error
+                    ? err.message
+                    : `Failed to recover broken symlink: ${String(err)}`,
+            });
+            continue;
+          }
+        }
+
+        const resolvedLinkedPath = path.isAbsolute(linkedPath)
+          ? linkedPath
+          : path.resolve(path.dirname(target), linkedPath);
+        const linkedTargetExists = await fs
+          .stat(resolvedLinkedPath)
+          .then(() => true)
+          .catch(() => false);
+
+        if (!linkedTargetExists) {
+          await fs.unlink(target);
+        } else {
+          summary.skipped.push(entry.name);
+          continue;
+        }
+      } else {
+        summary.skipped.push(entry.name);
+        continue;
+      }
     }
 
     try {
@@ -210,7 +248,7 @@ export function registerAgentCommands(program: Command): void {
 
           const installSummaries: SkillsInstallSummary[] = [];
           if (opts.installSkills !== false) {
-            const skillsDir = await resolvePaperclipSkillsDir();
+            const skillsDir = await resolvePaperclipSkillsDir(__moduleDir, [path.resolve(process.cwd(), "skills")]);
             if (!skillsDir) {
               throw new Error(
                 "Could not locate local Paperclip skills directory. Expected ./skills in the repo checkout.",
@@ -258,7 +296,7 @@ export function registerAgentCommands(program: Command): void {
           if (installSummaries.length > 0) {
             for (const summary of installSummaries) {
               console.log(
-                `${summary.tool}: linked=${summary.linked.length} skipped=${summary.skipped.length} failed=${summary.failed.length} target=${summary.target}`,
+                `${summary.tool}: linked=${summary.linked.length} removed=${summary.removed.length} skipped=${summary.skipped.length} failed=${summary.failed.length} target=${summary.target}`,
               );
               for (const failed of summary.failed) {
                 console.log(`  failed ${failed.name}: ${failed.error}`);

cli/src/commands/worktree.ts

@@ -83,6 +83,7 @@ type EmbeddedPostgresCtor = new (opts: {
   password: string;
   port: number;
   persistent: boolean;
+  initdbFlags?: string[];
   onLog?: (message: unknown) => void;
   onError?: (message: unknown) => void;
 }) => EmbeddedPostgresInstance;

doc/plans/2026-03-13-TOKEN-OPTIMIZATION-PLAN.md

@@ -0,0 +1,383 @@
+# Token Optimization Plan
+
+Date: 2026-03-13  
+Related discussion: https://github.com/paperclipai/paperclip/discussions/449
+
+## Goal
+
+Reduce token consumption materially without reducing agent capability, control-plane visibility, or task completion quality.
+
+This plan is based on:
+
+- the current V1 control-plane design
+- the current adapter and heartbeat implementation
+- the linked user discussion
+- local runtime data from the default Paperclip instance on 2026-03-13
+
+## Executive Summary
+
+The discussion is directionally right about two things:
+
+1. We should preserve session and prompt-cache locality more aggressively.
+2. We should separate stable startup instructions from per-heartbeat dynamic context.
+
+But that is not enough on its own.
+
+After reviewing the code and local run data, the token problem appears to have four distinct causes:
+
+1. **Measurement inflation on sessioned adapters.** Some token counters, especially for `codex_local`, appear to be recorded as cumulative session totals instead of per-heartbeat deltas.
+2. **Avoidable session resets.** Task sessions are intentionally reset on timer wakes and manual wakes, which destroys cache locality for common heartbeat paths.
+3. **Repeated context reacquisition.** The `paperclip` skill tells agents to re-fetch assignments, issue details, ancestors, and full comment threads on every heartbeat. The API does not currently offer efficient delta-oriented alternatives.
+4. **Large static instruction surfaces.** Agent instruction files and globally injected skills are reintroduced at startup even when most of that content is unchanged and not needed for the current task.
+
+The correct approach is:
+
+1. fix telemetry so we can trust the numbers
+2. preserve reuse where it is safe
+3. make context retrieval incremental
+4. add session compaction/rotation so long-lived sessions do not become progressively more expensive
+
+## Validated Findings
+
+### 1. Token telemetry is at least partly overstated today
+
+Observed from the local default instance:
+
+- `heartbeat_runs`: 11,360 runs between 2026-02-18 and 2026-03-13
+- summed `usage_json.inputTokens`: `2,272,142,368,952`
+- summed `usage_json.cachedInputTokens`: `2,217,501,559,420`
+
+Those totals are not credible as true per-heartbeat usage for the observed prompt sizes.
+
+Supporting evidence:
+
+- `adapter.invoke.payload.prompt` averages were small:
+  - `codex_local`: ~193 chars average, 6,067 chars max
+  - `claude_local`: ~160 chars average, 1,160 chars max
+- despite that, many `codex_local` runs report millions of input tokens
+- one reused Codex session in local data spans 3,607 runs and recorded `inputTokens` growing up to `1,155,283,166`
+
+Interpretation:
+
+- for sessioned adapters, especially Codex, we are likely storing usage reported by the runtime as a **session total**, not a **per-run delta**
+- this makes trend reporting, optimization work, and customer trust worse
+
+This does **not** mean there is no real token problem. It means we need a trustworthy baseline before we can judge optimization impact.
+
+### 2. Timer wakes currently throw away reusable task sessions
+
+In `server/src/services/heartbeat.ts`, `shouldResetTaskSessionForWake(...)` returns `true` for:
+
+- `wakeReason === "issue_assigned"`
+- `wakeSource === "timer"`
+- manual on-demand wakes
+
+That means many normal heartbeats skip saved task-session resume even when the workspace is stable.
+
+Local data supports the impact:
+
+- `timer/system` runs: 6,587 total
+- only 976 had a previous session
+- only 963 ended with the same session
+
+So timer wakes are the largest heartbeat path and are mostly not resuming prior task state.
+
+### 3. We repeatedly ask agents to reload the same task context
+
+The `paperclip` skill currently tells agents to do this on essentially every heartbeat:
+
+- fetch assignments
+- fetch issue details
+- fetch ancestor chain
+- fetch full issue comments
+
+Current API shape reinforces that pattern:
+
+- `GET /api/issues/:id/comments` returns the full thread
+- there is no `since`, cursor, digest, or summary endpoint for heartbeat consumption
+- `GET /api/issues/:id` returns full enriched issue context, not a minimal delta payload
+
+This is safe but expensive. It forces the model to repeatedly consume unchanged information.
+
+### 4. Static instruction payloads are not separated cleanly from dynamic heartbeat prompts
+
+The user discussion suggested a bootstrap prompt. That is the right direction.
+
+Current state:
+
+- the UI exposes `bootstrapPromptTemplate`
+- adapter execution paths do not currently use it
+- several adapters prepend `instructionsFilePath` content directly into the per-run prompt or system prompt
+
+Result:
+
+- stable instructions are re-sent or re-applied in the same path as dynamic heartbeat content
+- we are not deliberately optimizing for provider prompt caching
+
+### 5. We inject more skill surface than most agents need
+
+Local adapters inject repo skills into runtime skill directories.
+
+Current repo skill sizes:
+
+- `skills/paperclip/SKILL.md`: 17,441 bytes
+- `skills/create-agent-adapter/SKILL.md`: 31,832 bytes
+- `skills/paperclip-create-agent/SKILL.md`: 4,718 bytes
+- `skills/para-memory-files/SKILL.md`: 3,978 bytes
+
+That is nearly 58 KB of skill markdown before any company-specific instructions.
+
+Not all of that is necessarily loaded into model context every run, but it increases startup surface area and should be treated as a token budget concern.
+
+## Principles
+
+We should optimize tokens under these rules:
+
+1. **Do not lose functionality.** Agents must still be able to resume work safely, understand why tasks exist, and act within governance rules.
+2. **Prefer stable context over repeated context.** Unchanged instructions should not be resent through the most expensive path.
+3. **Prefer deltas over full reloads.** Heartbeats should consume only what changed since the last useful run.
+4. **Measure normalized deltas, not raw adapter claims.** Especially for sessioned CLIs.
+5. **Keep escape hatches.** Board/manual runs may still want a forced fresh session.
+
+## Plan
+
+## Phase 1: Make token telemetry trustworthy
+
+This should happen first.
+
+### Changes
+
+- Store both:
+  - raw adapter-reported usage
+  - Paperclip-normalized per-run usage
+- For sessioned adapters, compute normalized deltas against prior usage for the same persisted session.
+- Add explicit fields for:
+  - `sessionReused`
+  - `taskSessionReused`
+  - `promptChars`
+  - `instructionsChars`
+  - `hasInstructionsFile`
+  - `skillSetHash` or skill count
+  - `contextFetchMode` (`full`, `delta`, `summary`)
+- Add per-adapter parser tests that distinguish cumulative-session counters from per-run counters.
+
+### Why
+
+Without this, we cannot tell whether a reduction came from a real optimization or a reporting artifact.
+
+### Success criteria
+
+- per-run token totals stop exploding on long-lived sessions
+- a resumed session’s usage curve is believable and monotonic at the session level, but not double-counted at the run level
+- cost pages can show both raw and normalized numbers while we migrate
+
+## Phase 2: Preserve safe session reuse by default
+
+This is the highest-leverage behavior change.
+
+### Changes
+
+- Stop resetting task sessions on ordinary timer wakes.
+- Keep resetting on:
+  - explicit manual “fresh run” invocations
+  - assignment changes
+  - workspace mismatch
+  - model mismatch / invalid resume errors
+- Add an explicit wake flag like `forceFreshSession: true` when the board wants a reset.
+- Record why a session was reused or reset in run metadata.
+
+### Why
+
+Timer wakes are the dominant heartbeat path. Resetting them destroys both session continuity and prompt cache reuse.
+
+### Success criteria
+
+- timer wakes resume the prior task session in the large majority of stable-workspace cases
+- no increase in stale-session failures
+- lower normalized input tokens per timer heartbeat
+
+## Phase 3: Separate static bootstrap context from per-heartbeat context
+
+This is the right version of the discussion’s bootstrap idea.
+
+### Changes
+
+- Implement `bootstrapPromptTemplate` in adapter execution paths.
+- Use it only when starting a fresh session, not on resumed sessions.
+- Keep `promptTemplate` intentionally small and stable:
+  - who I am
+  - what triggered this wake
+  - which task/comment/approval to prioritize
+- Move long-lived setup text out of recurring per-run prompts where possible.
+- Add UI guidance and warnings when `promptTemplate` contains high-churn or large inline content.
+
+### Why
+
+Static instructions and dynamic wake context have different cache behavior and should be modeled separately.
+
+### Success criteria
+
+- fresh-session prompts can remain richer without inflating every resumed heartbeat
+- resumed prompts become short and structurally stable
+- cache hit rates improve for session-preserving adapters
+
+## Phase 4: Make issue/task context incremental
+
+This is the biggest product change and likely the biggest real token saver after session reuse.
+
+### Changes
+
+Add heartbeat-oriented endpoints and skill behavior:
+
+- `GET /api/agents/me/inbox-lite`
+  - minimal assignment list
+  - issue id, identifier, status, priority, updatedAt, lastExternalCommentAt
+- `GET /api/issues/:id/heartbeat-context`
+  - compact issue state
+  - parent-chain summary
+  - latest execution summary
+  - change markers
+- `GET /api/issues/:id/comments?after=<cursor>` or `?since=<timestamp>`
+  - return only new comments
+- optional `GET /api/issues/:id/context-digest`
+  - server-generated compact summary for heartbeat use
+
+Update the `paperclip` skill so the default pattern becomes:
+
+1. fetch compact inbox
+2. fetch compact task context
+3. fetch only new comments unless this is the first read, a mention-triggered wake, or a cache miss
+4. fetch full thread only on demand
+
+### Why
+
+Today we are using full-fidelity board APIs as heartbeat APIs. That is convenient but token-inefficient.
+
+### Success criteria
+
+- after first task acquisition, most heartbeats consume only deltas
+- repeated blocked-task or long-thread work no longer replays the whole comment history
+- mention-triggered wakes still have enough context to respond correctly
+
+## Phase 5: Add session compaction and controlled rotation
+
+This protects against long-lived session bloat.
+
+### Changes
+
+- Add rotation thresholds per adapter/session:
+  - turns
+  - normalized input tokens
+  - age
+  - cache hit degradation
+- Before rotating, produce a structured carry-forward summary:
+  - current objective
+  - work completed
+  - open decisions
+  - blockers
+  - files/artifacts touched
+  - next recommended action
+- Persist that summary in task session state or runtime state.
+- Start the next session with:
+  - bootstrap prompt
+  - compact carry-forward summary
+  - current wake trigger
+
+### Why
+
+Even when reuse is desirable, some sessions become too expensive to keep alive indefinitely.
+
+### Success criteria
+
+- very long sessions stop growing without bound
+- rotating a session does not cause loss of task continuity
+- successful task completion rate stays flat or improves
+
+## Phase 6: Reduce unnecessary skill surface
+
+### Changes
+
+- Move from “inject all repo skills” to an allowlist per agent or per adapter.
+- Default local runtime skill set should likely be:
+  - `paperclip`
+- Add opt-in skills for specialized agents:
+  - `paperclip-create-agent`
+  - `para-memory-files`
+  - `create-agent-adapter`
+- Expose active skill set in agent config and run metadata.
+
+### Why
+
+Most agents do not need adapter-authoring or memory-system skills on every run.
+
+### Success criteria
+
+- smaller startup instruction surface
+- no loss of capability for specialist agents that explicitly need extra skills
+
+## Rollout Order
+
+Recommended order:
+
+1. telemetry normalization
+2. timer-wake session reuse
+3. bootstrap prompt implementation
+4. heartbeat delta APIs + `paperclip` skill rewrite
+5. session compaction/rotation
+6. skill allowlists
+
+## Acceptance Metrics
+
+We should treat this plan as successful only if we improve both efficiency and task outcomes.
+
+Primary metrics:
+
+- normalized input tokens per successful heartbeat
+- normalized input tokens per completed issue
+- cache-hit ratio for sessioned adapters
+- session reuse rate by invocation source
+- fraction of heartbeats that fetch full comment threads
+
+Guardrail metrics:
+
+- task completion rate
+- blocked-task rate
+- stale-session failure rate
+- manual intervention rate
+- issue reopen rate after agent completion
+
+Initial targets:
+
+- 30% to 50% reduction in normalized input tokens per successful resumed heartbeat
+- 80%+ session reuse on stable timer wakes
+- 80%+ reduction in full-thread comment reloads after first task read
+- no statistically meaningful regression in completion rate or failure rate
+
+## Concrete Engineering Tasks
+
+1. Add normalized usage fields and migration support for run analytics.
+2. Patch sessioned adapter accounting to compute deltas from prior session totals.
+3. Change `shouldResetTaskSessionForWake(...)` so timer wakes do not reset by default.
+4. Implement `bootstrapPromptTemplate` end-to-end in adapter execution.
+5. Add compact heartbeat context and incremental comment APIs.
+6. Rewrite `skills/paperclip/SKILL.md` around delta-fetch behavior.
+7. Add session rotation with carry-forward summaries.
+8. Replace global skill injection with explicit allowlists.
+
+## Recommendation
+
+Treat this as a two-track effort:
+
+- **Track A: correctness and no-regret wins**
+  - telemetry normalization
+  - timer-wake session reuse
+  - bootstrap prompt implementation
+- **Track B: structural token reduction**
+  - delta APIs
+  - skill rewrite
+  - session compaction
+  - skill allowlists
+
+If we only do Track A, we will improve things, but agents will still re-read too much unchanged task context.
+
+If we only do Track B without fixing telemetry first, we will not be able to prove the gains cleanly.

packages/adapter-utils/src/server-utils.ts

@@ -32,6 +32,23 @@ export const runningProcesses = new Map<string, RunningProcess>();
 export const MAX_CAPTURE_BYTES = 4 * 1024 * 1024;
 export const MAX_EXCERPT_BYTES = 32 * 1024;
 const SENSITIVE_ENV_KEY = /(key|token|secret|password|passwd|authorization|cookie)/i;
+const PAPERCLIP_SKILL_ROOT_RELATIVE_CANDIDATES = [
+  "../../skills",
+  "../../../../../skills",
+];
+
+export interface PaperclipSkillEntry {
+  name: string;
+  source: string;
+}
+
+function normalizePathSlashes(value: string): string {
+  return value.replaceAll("\\", "/");
+}
+
+function isMaintainerOnlySkillTarget(candidate: string): boolean {
+  return normalizePathSlashes(candidate).includes("/.agents/skills/");
+}
 
 export function parseObject(value: unknown): Record<string, unknown> {
   if (typeof value !== "object" || value === null || Array.isArray(value)) {
@@ -245,6 +262,136 @@ export async function ensureAbsoluteDirectory(
   }
 }
 
+export async function resolvePaperclipSkillsDir(
+  moduleDir: string,
+  additionalCandidates: string[] = [],
+): Promise<string | null> {
+  const candidates = [
+    ...PAPERCLIP_SKILL_ROOT_RELATIVE_CANDIDATES.map((relativePath) => path.resolve(moduleDir, relativePath)),
+    ...additionalCandidates.map((candidate) => path.resolve(candidate)),
+  ];
+  const seenRoots = new Set<string>();
+
+  for (const root of candidates) {
+    if (seenRoots.has(root)) continue;
+    seenRoots.add(root);
+    const isDirectory = await fs.stat(root).then((stats) => stats.isDirectory()).catch(() => false);
+    if (isDirectory) return root;
+  }
+
+  return null;
+}
+
+export async function listPaperclipSkillEntries(
+  moduleDir: string,
+  additionalCandidates: string[] = [],
+): Promise<PaperclipSkillEntry[]> {
+  const root = await resolvePaperclipSkillsDir(moduleDir, additionalCandidates);
+  if (!root) return [];
+
+  try {
+    const entries = await fs.readdir(root, { withFileTypes: true });
+    return entries
+      .filter((entry) => entry.isDirectory())
+      .map((entry) => ({
+        name: entry.name,
+        source: path.join(root, entry.name),
+      }));
+  } catch {
+    return [];
+  }
+}
+
+export async function readPaperclipSkillMarkdown(
+  moduleDir: string,
+  skillName: string,
+): Promise<string | null> {
+  const normalized = skillName.trim().toLowerCase();
+  if (!normalized) return null;
+
+  const entries = await listPaperclipSkillEntries(moduleDir);
+  const match = entries.find((entry) => entry.name === normalized);
+  if (!match) return null;
+
+  try {
+    return await fs.readFile(path.join(match.source, "SKILL.md"), "utf8");
+  } catch {
+    return null;
+  }
+}
+
+export async function ensurePaperclipSkillSymlink(
+  source: string,
+  target: string,
+  linkSkill: (source: string, target: string) => Promise<void> = (linkSource, linkTarget) =>
+    fs.symlink(linkSource, linkTarget),
+): Promise<"created" | "repaired" | "skipped"> {
+  const existing = await fs.lstat(target).catch(() => null);
+  if (!existing) {
+    await linkSkill(source, target);
+    return "created";
+  }
+
+  if (!existing.isSymbolicLink()) {
+    return "skipped";
+  }
+
+  const linkedPath = await fs.readlink(target).catch(() => null);
+  if (!linkedPath) return "skipped";
+
+  const resolvedLinkedPath = path.resolve(path.dirname(target), linkedPath);
+  if (resolvedLinkedPath === source) {
+    return "skipped";
+  }
+
+  const linkedPathExists = await fs.stat(resolvedLinkedPath).then(() => true).catch(() => false);
+  if (linkedPathExists) {
+    return "skipped";
+  }
+
+  await fs.unlink(target);
+  await linkSkill(source, target);
+  return "repaired";
+}
+
+export async function removeMaintainerOnlySkillSymlinks(
+  skillsHome: string,
+  allowedSkillNames: Iterable<string>,
+): Promise<string[]> {
+  const allowed = new Set(Array.from(allowedSkillNames));
+  try {
+    const entries = await fs.readdir(skillsHome, { withFileTypes: true });
+    const removed: string[] = [];
+    for (const entry of entries) {
+      if (allowed.has(entry.name)) continue;
+
+      const target = path.join(skillsHome, entry.name);
+      const existing = await fs.lstat(target).catch(() => null);
+      if (!existing?.isSymbolicLink()) continue;
+
+      const linkedPath = await fs.readlink(target).catch(() => null);
+      if (!linkedPath) continue;
+
+      const resolvedLinkedPath = path.isAbsolute(linkedPath)
+        ? linkedPath
+        : path.resolve(path.dirname(target), linkedPath);
+      if (
+        !isMaintainerOnlySkillTarget(linkedPath) &&
+        !isMaintainerOnlySkillTarget(resolvedLinkedPath)
+      ) {
+        continue;
+      }
+
+      await fs.unlink(target);
+      removed.push(entry.name);
+    }
+
+    return removed;
+  } catch {
+    return [];
+  }
+}
+
 export async function ensureCommandResolvable(command: string, cwd: string, env: NodeJS.ProcessEnv) {
   const resolved = await resolveCommandPath(command, cwd, env);
   if (resolved) return;

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

@@ -13,17 +13,16 @@ import {
   redactEnvForLogs,
   ensureAbsoluteDirectory,
   ensureCommandResolvable,
+  ensurePaperclipSkillSymlink,
   ensurePathInEnv,
+  listPaperclipSkillEntries,
+  removeMaintainerOnlySkillSymlinks,
   renderTemplate,
   runChildProcess,
 } from "@paperclipai/adapter-utils/server-utils";
 import { parseCodexJsonl, isCodexUnknownSessionError } from "./parse.js";
 
 const __moduleDir = path.dirname(fileURLToPath(import.meta.url));
-const PAPERCLIP_SKILLS_CANDIDATES = [
-  path.resolve(__moduleDir, "../../skills"),         // published: <pkg>/dist/server/ -> <pkg>/skills/
-  path.resolve(__moduleDir, "../../../../../skills"), // dev: src/server/ -> repo root/skills/
-];
 const CODEX_ROLLOUT_NOISE_RE =
   /^\d{4}-\d{2}-\d{2}T[^\s]+\s+ERROR\s+codex_core::rollout::list:\s+state db missing rollout path for thread\s+[a-z0-9-]+$/i;
 
@@ -67,33 +66,42 @@ function codexHomeDir(): string {
   return path.join(os.homedir(), ".codex");
 }
 
-async function resolvePaperclipSkillsDir(): Promise<string | null> {
-  for (const candidate of PAPERCLIP_SKILLS_CANDIDATES) {
-    const isDir = await fs.stat(candidate).then((s) => s.isDirectory()).catch(() => false);
-    if (isDir) return candidate;
-  }
-  return null;
-}
+type EnsureCodexSkillsInjectedOptions = {
+  skillsHome?: string;
+  skillsEntries?: Awaited<ReturnType<typeof listPaperclipSkillEntries>>;
+  linkSkill?: (source: string, target: string) => Promise<void>;
+};
 
-async function ensureCodexSkillsInjected(onLog: AdapterExecutionContext["onLog"]) {
-  const skillsDir = await resolvePaperclipSkillsDir();
-  if (!skillsDir) return;
+export async function ensureCodexSkillsInjected(
+  onLog: AdapterExecutionContext["onLog"],
+  options: EnsureCodexSkillsInjectedOptions = {},
+) {
+  const skillsEntries = options.skillsEntries ?? await listPaperclipSkillEntries(__moduleDir);
+  if (skillsEntries.length === 0) return;
 
-  const skillsHome = path.join(codexHomeDir(), "skills");
+  const skillsHome = options.skillsHome ?? path.join(codexHomeDir(), "skills");
   await fs.mkdir(skillsHome, { recursive: true });
-  const entries = await fs.readdir(skillsDir, { withFileTypes: true });
-  for (const entry of entries) {
-    if (!entry.isDirectory()) continue;
-    const source = path.join(skillsDir, entry.name);
+  const removedSkills = await removeMaintainerOnlySkillSymlinks(
+    skillsHome,
+    skillsEntries.map((entry) => entry.name),
+  );
+  for (const skillName of removedSkills) {
+    await onLog(
+      "stderr",
+      `[paperclip] Removed maintainer-only Codex skill "${skillName}" from ${skillsHome}\n`,
+    );
+  }
+  const linkSkill = options.linkSkill;
+  for (const entry of skillsEntries) {
     const target = path.join(skillsHome, entry.name);
-    const existing = await fs.lstat(target).catch(() => null);
-    if (existing) continue;
 
     try {
-      await fs.symlink(source, target);
+      const result = await ensurePaperclipSkillSymlink(entry.source, target, linkSkill);
+      if (result === "skipped") continue;
+
       await onLog(
         "stderr",
-        `[paperclip] Injected Codex skill "${entry.name}" into ${skillsHome}\n`,
+        `[paperclip] ${result === "repaired" ? "Repaired" : "Injected"} Codex skill "${entry.name}" into ${skillsHome}\n`,
       );
     } catch (err) {
       await onLog(

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

@@ -1,4 +1,4 @@
-export { execute } from "./execute.js";
+export { execute, ensureCodexSkillsInjected } from "./execute.js";
 export { testEnvironment } from "./test.js";
 export { parseCodexJsonl, isCodexUnknownSessionError } from "./parse.js";
 import type { AdapterSessionCodec } from "@paperclipai/adapter-utils";

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

@@ -1,5 +1,4 @@
 import fs from "node:fs/promises";
-import type { Dirent } from "node:fs";
 import os from "node:os";
 import path from "node:path";
 import { fileURLToPath } from "node:url";
@@ -13,7 +12,10 @@ import {
   redactEnvForLogs,
   ensureAbsoluteDirectory,
   ensureCommandResolvable,
+  ensurePaperclipSkillSymlink,
   ensurePathInEnv,
+  listPaperclipSkillEntries,
+  removeMaintainerOnlySkillSymlinks,
   renderTemplate,
   runChildProcess,
 } from "@paperclipai/adapter-utils/server-utils";
@@ -23,10 +25,6 @@ import { normalizeCursorStreamLine } from "../shared/stream.js";
 import { hasCursorTrustBypassArg } from "../shared/trust.js";
 
 const __moduleDir = path.dirname(fileURLToPath(import.meta.url));
-const PAPERCLIP_SKILLS_CANDIDATES = [
-  path.resolve(__moduleDir, "../../skills"),
-  path.resolve(__moduleDir, "../../../../../skills"),
-];
 
 function firstNonEmptyLine(text: string): string {
   return (
@@ -82,16 +80,9 @@ function cursorSkillsHome(): string {
   return path.join(os.homedir(), ".cursor", "skills");
 }
 
-async function resolvePaperclipSkillsDir(): Promise<string | null> {
-  for (const candidate of PAPERCLIP_SKILLS_CANDIDATES) {
-    const isDir = await fs.stat(candidate).then((s) => s.isDirectory()).catch(() => false);
-    if (isDir) return candidate;
-  }
-  return null;
-}
-
 type EnsureCursorSkillsInjectedOptions = {
   skillsDir?: string | null;
+  skillsEntries?: Array<{ name: string; source: string }>;
   skillsHome?: string;
   linkSkill?: (source: string, target: string) => Promise<void>;
 };
@@ -100,8 +91,13 @@ export async function ensureCursorSkillsInjected(
   onLog: AdapterExecutionContext["onLog"],
   options: EnsureCursorSkillsInjectedOptions = {},
 ) {
-  const skillsDir = options.skillsDir ?? await resolvePaperclipSkillsDir();
-  if (!skillsDir) return;
+  const skillsEntries = options.skillsEntries
+    ?? (options.skillsDir
+      ? (await fs.readdir(options.skillsDir, { withFileTypes: true }))
+          .filter((entry) => entry.isDirectory())
+          .map((entry) => ({ name: entry.name, source: path.join(options.skillsDir!, entry.name) }))
+      : await listPaperclipSkillEntries(__moduleDir));
+  if (skillsEntries.length === 0) return;
 
   const skillsHome = options.skillsHome ?? cursorSkillsHome();
   try {
@@ -113,31 +109,26 @@ export async function ensureCursorSkillsInjected(
     );
     return;
   }
-
-  let entries: Dirent[];
-  try {
-    entries = await fs.readdir(skillsDir, { withFileTypes: true });
-  } catch (err) {
+  const removedSkills = await removeMaintainerOnlySkillSymlinks(
+    skillsHome,
+    skillsEntries.map((entry) => entry.name),
+  );
+  for (const skillName of removedSkills) {
     await onLog(
       "stderr",
-      `[paperclip] Failed to read Paperclip skills from ${skillsDir}: ${err instanceof Error ? err.message : String(err)}\n`,
+      `[paperclip] Removed maintainer-only Cursor skill "${skillName}" from ${skillsHome}\n`,
     );
-    return;
   }
-
   const linkSkill = options.linkSkill ?? ((source: string, target: string) => fs.symlink(source, target));
-  for (const entry of entries) {
-    if (!entry.isDirectory()) continue;
-    const source = path.join(skillsDir, entry.name);
+  for (const entry of skillsEntries) {
     const target = path.join(skillsHome, entry.name);
-    const existing = await fs.lstat(target).catch(() => null);
-    if (existing) continue;
-
     try {
-      await linkSkill(source, target);
+      const result = await ensurePaperclipSkillSymlink(entry.source, target, linkSkill);
+      if (result === "skipped") continue;
+
       await onLog(
         "stderr",
-        `[paperclip] Injected Cursor skill "${entry.name}" into ${skillsHome}\n`,
+        `[paperclip] ${result === "repaired" ? "Repaired" : "Injected"} Cursor skill "${entry.name}" into ${skillsHome}\n`,
       );
     } catch (err) {
       await onLog(

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

@@ -12,7 +12,10 @@ import {
   buildPaperclipEnv,
   ensureAbsoluteDirectory,
   ensureCommandResolvable,
+  ensurePaperclipSkillSymlink,
   ensurePathInEnv,
+  listPaperclipSkillEntries,
+  removeMaintainerOnlySkillSymlinks,
   parseObject,
   redactEnvForLogs,
   renderTemplate,
@@ -29,10 +32,6 @@ import {
 import { firstNonEmptyLine } from "./utils.js";
 
 const __moduleDir = path.dirname(fileURLToPath(import.meta.url));
-const PAPERCLIP_SKILLS_CANDIDATES = [
-  path.resolve(__moduleDir, "../../skills"),
-  path.resolve(__moduleDir, "../../../../../skills"),
-];
 
 function hasNonEmptyEnvValue(env: Record<string, string>, key: string): boolean {
   const raw = env[key];
@@ -73,14 +72,6 @@ function renderApiAccessNote(env: Record<string, string>): string {
   ].join("\n");
 }
 
-async function resolvePaperclipSkillsDir(): Promise<string | null> {
-  for (const candidate of PAPERCLIP_SKILLS_CANDIDATES) {
-    const isDir = await fs.stat(candidate).then((s) => s.isDirectory()).catch(() => false);
-    if (isDir) return candidate;
-  }
-  return null;
-}
-
 function geminiSkillsHome(): string {
   return path.join(os.homedir(), ".gemini", "skills");
 }
@@ -93,8 +84,8 @@ function geminiSkillsHome(): string {
 async function ensureGeminiSkillsInjected(
   onLog: AdapterExecutionContext["onLog"],
 ): Promise<void> {
-  const skillsDir = await resolvePaperclipSkillsDir();
-  if (!skillsDir) return;
+  const skillsEntries = await listPaperclipSkillEntries(__moduleDir);
+  if (skillsEntries.length === 0) return;
 
   const skillsHome = geminiSkillsHome();
   try {
@@ -106,28 +97,27 @@ async function ensureGeminiSkillsInjected(
     );
     return;
   }
-
-  let entries: Dirent[];
-  try {
-    entries = await fs.readdir(skillsDir, { withFileTypes: true });
-  } catch (err) {
+  const removedSkills = await removeMaintainerOnlySkillSymlinks(
+    skillsHome,
+    skillsEntries.map((entry) => entry.name),
+  );
+  for (const skillName of removedSkills) {
     await onLog(
       "stderr",
-      `[paperclip] Failed to read Paperclip skills from ${skillsDir}: ${err instanceof Error ? err.message : String(err)}\n`,
+      `[paperclip] Removed maintainer-only Gemini skill "${skillName}" from ${skillsHome}\n`,
     );
-    return;
   }
 
-  for (const entry of entries) {
-    if (!entry.isDirectory()) continue;
-    const source = path.join(skillsDir, entry.name);
+  for (const entry of skillsEntries) {
     const target = path.join(skillsHome, entry.name);
-    const existing = await fs.lstat(target).catch(() => null);
-    if (existing) continue;
 
     try {
-      await fs.symlink(source, target);
-      await onLog("stderr", `[paperclip] Linked Gemini skill: ${entry.name}\n`);
+      const result = await ensurePaperclipSkillSymlink(entry.source, target);
+      if (result === "skipped") continue;
+      await onLog(
+        "stderr",
+        `[paperclip] ${result === "repaired" ? "Repaired" : "Linked"} Gemini skill: ${entry.name}\n`,
+      );
     } catch (err) {
       await onLog(
         "stderr",

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

@@ -12,7 +12,10 @@ import {
   redactEnvForLogs,
   ensureAbsoluteDirectory,
   ensureCommandResolvable,
+  ensurePaperclipSkillSymlink,
   ensurePathInEnv,
+  listPaperclipSkillEntries,
+  removeMaintainerOnlySkillSymlinks,
   renderTemplate,
   runChildProcess,
 } from "@paperclipai/adapter-utils/server-utils";
@@ -20,10 +23,6 @@ import { isPiUnknownSessionError, parsePiJsonl } from "./parse.js";
 import { ensurePiModelConfiguredAndAvailable } from "./models.js";
 
 const __moduleDir = path.dirname(fileURLToPath(import.meta.url));
-const PAPERCLIP_SKILLS_CANDIDATES = [
-  path.resolve(__moduleDir, "../../skills"),
-  path.resolve(__moduleDir, "../../../../../skills"),
-];
 
 const PAPERCLIP_SESSIONS_DIR = path.join(os.homedir(), ".pi", "paperclips");
 
@@ -50,34 +49,32 @@ function parseModelId(model: string | null): string | null {
   return trimmed.slice(trimmed.indexOf("/") + 1).trim() || null;
 }
 
-async function resolvePaperclipSkillsDir(): Promise<string | null> {
-  for (const candidate of PAPERCLIP_SKILLS_CANDIDATES) {
-    const isDir = await fs.stat(candidate).then((s) => s.isDirectory()).catch(() => false);
-    if (isDir) return candidate;
-  }
-  return null;
-}
-
 async function ensurePiSkillsInjected(onLog: AdapterExecutionContext["onLog"]) {
-  const skillsDir = await resolvePaperclipSkillsDir();
-  if (!skillsDir) return;
+  const skillsEntries = await listPaperclipSkillEntries(__moduleDir);
+  if (skillsEntries.length === 0) return;
 
   const piSkillsHome = path.join(os.homedir(), ".pi", "agent", "skills");
   await fs.mkdir(piSkillsHome, { recursive: true });
-  
-  const entries = await fs.readdir(skillsDir, { withFileTypes: true });
-  for (const entry of entries) {
-    if (!entry.isDirectory()) continue;
-    const source = path.join(skillsDir, entry.name);
+  const removedSkills = await removeMaintainerOnlySkillSymlinks(
+    piSkillsHome,
+    skillsEntries.map((entry) => entry.name),
+  );
+  for (const skillName of removedSkills) {
+    await onLog(
+      "stderr",
+      `[paperclip] Removed maintainer-only Pi skill "${skillName}" from ${piSkillsHome}\n`,
+    );
+  }
+
+  for (const entry of skillsEntries) {
     const target = path.join(piSkillsHome, entry.name);
-    const existing = await fs.lstat(target).catch(() => null);
-    if (existing) continue;
 
     try {
-      await fs.symlink(source, target);
+      const result = await ensurePaperclipSkillSymlink(entry.source, target);
+      if (result === "skipped") continue;
       await onLog(
         "stderr",
-        `[paperclip] Injected Pi skill "${entry.name}" into ${piSkillsHome}\n`,
+        `[paperclip] ${result === "repaired" ? "Repaired" : "Injected"} Pi skill "${entry.name}" into ${piSkillsHome}\n`,
       );
     } catch (err) {
       await onLog(

packages/db/src/migration-runtime.ts

@@ -17,6 +17,7 @@ type EmbeddedPostgresCtor = new (opts: {
   password: string;
   port: number;
   persistent: boolean;
+  initdbFlags?: string[];
   onLog?: (message: unknown) => void;
   onError?: (message: unknown) => void;
 }) => EmbeddedPostgresInstance;

server/src/__tests__/paperclip-skill-utils.test.ts

@@ -0,0 +1,61 @@
+import fs from "node:fs/promises";
+import os from "node:os";
+import path from "node:path";
+import { afterEach, describe, expect, it } from "vitest";
+import {
+  listPaperclipSkillEntries,
+  removeMaintainerOnlySkillSymlinks,
+} from "@paperclipai/adapter-utils/server-utils";
+
+async function makeTempDir(prefix: string): Promise<string> {
+  return fs.mkdtemp(path.join(os.tmpdir(), prefix));
+}
+
+describe("paperclip skill utils", () => {
+  const cleanupDirs = new Set<string>();
+
+  afterEach(async () => {
+    await Promise.all(Array.from(cleanupDirs).map((dir) => fs.rm(dir, { recursive: true, force: true })));
+    cleanupDirs.clear();
+  });
+
+  it("lists runtime skills from ./skills without pulling in .agents/skills", async () => {
+    const root = await makeTempDir("paperclip-skill-roots-");
+    cleanupDirs.add(root);
+
+    const moduleDir = path.join(root, "a", "b", "c", "d", "e");
+    await fs.mkdir(moduleDir, { recursive: true });
+    await fs.mkdir(path.join(root, "skills", "paperclip"), { recursive: true });
+    await fs.mkdir(path.join(root, ".agents", "skills", "release"), { recursive: true });
+
+    const entries = await listPaperclipSkillEntries(moduleDir);
+
+    expect(entries.map((entry) => entry.name)).toEqual(["paperclip"]);
+    expect(entries[0]?.source).toBe(path.join(root, "skills", "paperclip"));
+  });
+
+  it("removes stale maintainer-only symlinks from a shared skills home", async () => {
+    const root = await makeTempDir("paperclip-skill-cleanup-");
+    cleanupDirs.add(root);
+
+    const skillsHome = path.join(root, "skills-home");
+    const runtimeSkill = path.join(root, "skills", "paperclip");
+    const customSkill = path.join(root, "custom", "release-notes");
+    const staleMaintainerSkill = path.join(root, ".agents", "skills", "release");
+
+    await fs.mkdir(skillsHome, { recursive: true });
+    await fs.mkdir(runtimeSkill, { recursive: true });
+    await fs.mkdir(customSkill, { recursive: true });
+
+    await fs.symlink(runtimeSkill, path.join(skillsHome, "paperclip"));
+    await fs.symlink(customSkill, path.join(skillsHome, "release-notes"));
+    await fs.symlink(staleMaintainerSkill, path.join(skillsHome, "release"));
+
+    const removed = await removeMaintainerOnlySkillSymlinks(skillsHome, ["paperclip"]);
+
+    expect(removed).toEqual(["release"]);
+    await expect(fs.lstat(path.join(skillsHome, "release"))).rejects.toThrow();
+    expect((await fs.lstat(path.join(skillsHome, "paperclip"))).isSymbolicLink()).toBe(true);
+    expect((await fs.lstat(path.join(skillsHome, "release-notes"))).isSymbolicLink()).toBe(true);
+  });
+});