chore(paths): refactor data directory structure and update references

- Updated paths for instance data, workflows, and logs to use a unified `data/` directory.
- Adjusted related documentation in AGENTS.md and README.md to reflect the new data structure.
- Refactored path handling in server files to ensure consistency and clarity in data management.
- Enhanced test scripts to align with the new directory structure for improved organization.

packages/server/app-version.js

@@ -1,8 +1,8 @@
 import fs from "fs";
 import path from "path";
-import { SERVER_ROOT } from "./paths.js";
+import { REPO_ROOT } from "./paths.js";
 
-const ROOT_PKG = path.resolve(SERVER_ROOT, "../../package.json");
+const ROOT_PKG = path.join(REPO_ROOT, "package.json");
 
 /**
  * JerapahFlow app version from the monorepo root package.json.

packages/server/package.json

@@ -13,8 +13,8 @@
     "start:control": "node control.js",
     "start:web": "node web-server.js",
     "migrate": "node -e \"import('./db.js').then((m) => m.migrate().then(() => process.exit(0)))\"",
-    "test:plugins": "JFLOW_PLUGINS_DIR=./data/plugins-smoke-test JFLOW_DB_PATH=./data/plugins-smoke.db node test/plugins-smoke.js",
-    "test:workflow-history": "JFLOW_WORKFLOWS_DIR=./data/workflow-history-smoke JFLOW_DB_PATH=./data/workflow-history-smoke.db node test/workflow-history-smoke.js",
+    "test:plugins": "JFLOW_DATA_DIR=./data JFLOW_PLUGINS_DIR=./data/plugins-smoke-test JFLOW_DB_PATH=./data/plugins-smoke.db node test/plugins-smoke.js",
+    "test:workflow-history": "JFLOW_DATA_DIR=./data JFLOW_WORKFLOWS_DIR=./data/workflow-history-smoke JFLOW_DB_PATH=./data/workflow-history-smoke.db node test/workflow-history-smoke.js",
     "reset-admin": "node reset-admin.js",
     "test:profiles": "node test/profiles-smoke.js",
     "test:set-dry-run": "node test/set-dry-run-smoke.js",

packages/server/paths.js

@@ -1,25 +1,49 @@
+import fs from "fs";
 import path from "path";
 import { fileURLToPath } from "url";
 
 export const SERVER_ROOT = path.dirname(fileURLToPath(import.meta.url));
+export const REPO_ROOT = path.resolve(SERVER_ROOT, "../..");
 export const SCRIPTS_DIR = path.join(SERVER_ROOT, "scripts");
-export const DATA_DIR = path.join(SERVER_ROOT, "data");
+
+/** Prefer `preferred` unless only `legacy` already has files. */
+function existingDir(preferred, legacy, probe) {
+  const has = (dir) =>
+    probe ? probe(dir) : fs.existsSync(dir);
+  if (has(preferred) || !has(legacy)) return preferred;
+  return legacy;
+}
+
+function hasInstanceData(dir) {
+  return (
+    fs.existsSync(path.join(dir, "jerapah-flow.db")) ||
+    fs.existsSync(path.join(dir, "workflows"))
+  );
+}
+
+/** Instance data (SQLite, live workflows, control-state). Not product source. */
+export const DATA_DIR = path.resolve(
+  process.env.JFLOW_DATA_DIR ??
+    existingDir(
+      path.join(REPO_ROOT, "data"),
+      path.join(SERVER_ROOT, "data"),
+      hasInstanceData,
+    ),
+);
 /** Live instance workflows (not shipped in git). Override for tests. */
-export const WORKFLOWS_DIR =
-  process.env.JFLOW_WORKFLOWS_DIR ?? path.join(DATA_DIR, "workflows");
+export const WORKFLOWS_DIR = path.resolve(
+  process.env.JFLOW_WORKFLOWS_DIR ?? path.join(DATA_DIR, "workflows"),
+);
 /** User plugins (repo-root /plugins, outside the pnpm workspace). */
-export const PLUGINS_DIR =
-  process.env.JFLOW_PLUGINS_DIR ??
-  path.resolve(SERVER_ROOT, "../../plugins");
+export const PLUGINS_DIR = path.resolve(
+  process.env.JFLOW_PLUGINS_DIR ?? path.join(REPO_ROOT, "plugins"),
+);
 /** Example plugin sources shipped with the repo. */
-export const EXAMPLE_PLUGINS_DIR = path.resolve(
-  SERVER_ROOT,
-  "../../examples/plugins",
-);
+export const EXAMPLE_PLUGINS_DIR = path.join(REPO_ROOT, "examples/plugins");
 /** Example workflow YAML presets (not loaded by the runner). */
-export const EXAMPLE_WORKFLOWS_DIR = path.resolve(
-  SERVER_ROOT,
-  "../../examples/workflows",
+export const EXAMPLE_WORKFLOWS_DIR = path.join(REPO_ROOT, "examples/workflows");
+export const LOGS_DIR = path.resolve(
+  process.env.JFLOW_LOGS_DIR ??
+    existingDir(path.join(REPO_ROOT, "logs"), path.join(SERVER_ROOT, "logs")),
 );
-export const LOGS_DIR = path.join(SERVER_ROOT, "logs");
-export const WEB_DIST = path.resolve(SERVER_ROOT, "../web/dist");
+export const WEB_DIST = path.join(REPO_ROOT, "packages/web/dist");

packages/server/pm2-bridge.js

@@ -1,8 +1,6 @@
 import path from "path";
 import pm2 from "pm2";
-import { SERVER_ROOT } from "./paths.js";
-
-const REPO_ROOT = path.resolve(SERVER_ROOT, "../..");
+import { REPO_ROOT, SERVER_ROOT } from "./paths.js";
 
 export const PM2_HTTP_NAME = "jflow-http";
 export const PM2_WORKER_NAME = "jflow-worker";

packages/server/test/plugins-smoke.js

@@ -2,6 +2,7 @@
  * Smoke: core vs plugin scripts, fork, example install, resolve, run.
  *
  * Run:
+ *   JFLOW_DATA_DIR=packages/server/data \
  *   JFLOW_PLUGINS_DIR=packages/server/data/plugins-smoke-test \
  *   JFLOW_DB_PATH=packages/server/data/plugins-smoke.db \
  *   node packages/server/test/plugins-smoke.js