Remove SQLite/Drizzle infrastructure from dev branch

Strip all database dependencies and revert to main's file-backed stores:
- Delete packages/server/src/server/db/ (schema, migrations, DB stores, legacy importers)
- Remove better-sqlite3, drizzle-orm, drizzle-kit, @electron/rebuild deps
- Revert bootstrap.ts to FileBackedProjectRegistry/WorkspaceRegistry/AgentStorage
- Restore workspace-registry-bootstrap.ts from main
- Revert AgentSnapshotStore → AgentStorage across all files
- Fix session.ts field names (directory→cwd, numeric id→string workspaceId)
- Remove DB-only tests from bootstrap.smoke.test, agent-manager.test, etc.

packages/server/scripts/db-query.ts

@@ -1,140 +0,0 @@
-#!/usr/bin/env npx tsx
-/**
- * Run arbitrary SQL against the Paseo SQLite database.
- *
- * Usage:
- *   npx tsx packages/server/scripts/db-query.ts "SELECT * FROM agent_snapshots"
- *   npx tsx packages/server/scripts/db-query.ts --db ~/.paseo/db "SELECT count(*) FROM agent_timeline_rows"
- *
- * Without args, shows table row counts.
- */
-
-import path from "node:path";
-import os from "node:os";
-import fs from "node:fs";
-import Database from "better-sqlite3";
-
-function resolveHomeDirectory(value: string): string {
-  if (value === "~") {
-    return os.homedir();
-  }
-
-  if (value.startsWith("~/")) {
-    return path.join(os.homedir(), value.slice(2));
-  }
-
-  return value;
-}
-
-function parseListenPort(listen: unknown): number | null {
-  if (typeof listen !== "string") {
-    return null;
-  }
-
-  const portMatch = listen.match(/:(\d+)$/);
-  return portMatch ? parseInt(portMatch[1]!, 10) : null;
-}
-
-function findDevDatabaseDirectory(): string | null {
-  const tmpDir = os.tmpdir();
-  for (const entry of fs.readdirSync(tmpDir)) {
-    if (entry.startsWith("paseo-dev.")) {
-      const configPath = path.join(tmpDir, entry, "config.json");
-      if (fs.existsSync(configPath)) {
-        try {
-          const config = JSON.parse(fs.readFileSync(configPath, "utf-8"));
-          const dbDir = config.paseoHome ? path.join(config.paseoHome, "db") : null;
-          const port = parseListenPort(config.daemon?.listen);
-          if (dbDir && port === 6767) {
-            return dbDir;
-          }
-        } catch {}
-      }
-    }
-  }
-
-  return null;
-}
-
-function resolveDatabasePath(explicitPath?: string): string {
-  if (explicitPath) {
-    const resolvedPath = path.resolve(resolveHomeDirectory(explicitPath));
-    return fs.statSync(resolvedPath).isDirectory()
-      ? path.join(resolvedPath, "paseo.sqlite")
-      : resolvedPath;
-  }
-
-  const detectedDevDir = findDevDatabaseDirectory();
-  if (detectedDevDir) {
-    return path.join(detectedDevDir, "paseo.sqlite");
-  }
-
-  const paseoHome = process.env.PASEO_HOME
-    ? path.resolve(resolveHomeDirectory(process.env.PASEO_HOME))
-    : path.join(os.homedir(), ".paseo");
-  return path.join(paseoHome, "db", "paseo.sqlite");
-}
-
-async function main() {
-  const args = process.argv.slice(2);
-  let dbPath: string | undefined;
-  const queries: string[] = [];
-
-  for (let i = 0; i < args.length; i++) {
-    if (args[i] === "--db" && args[i + 1]) {
-      dbPath = args[++i];
-    } else {
-      queries.push(args[i]!);
-    }
-  }
-
-  if (queries.length === 0) {
-    queries.push(
-      "SELECT 'agent_snapshots' AS table_name, count(*) AS rows FROM agent_snapshots UNION ALL " +
-        "SELECT 'agent_timeline_rows', count(*) FROM agent_timeline_rows UNION ALL " +
-        "SELECT 'projects', count(*) FROM projects UNION ALL " +
-        "SELECT 'workspaces', count(*) FROM workspaces " +
-        "ORDER BY table_name",
-    );
-  }
-
-  let databasePath = "";
-  let client: Database.Database | null = null;
-
-  try {
-    if (dbPath) {
-      const resolvedDbPath = path.resolve(resolveHomeDirectory(dbPath));
-      databasePath =
-        fs.existsSync(resolvedDbPath) && fs.statSync(resolvedDbPath).isDirectory()
-          ? path.join(resolvedDbPath, "paseo.sqlite")
-          : resolvedDbPath;
-    } else {
-      databasePath = resolveDatabasePath();
-    }
-
-    client = new Database(databasePath, { readonly: true, fileMustExist: true });
-
-    for (const sql of queries) {
-      const statement = client.prepare(sql);
-      if (statement.reader) {
-        const rows = statement.all();
-        if (rows.length === 0) {
-          console.log("(0 rows)\n");
-        } else {
-          console.table(rows);
-        }
-        continue;
-      }
-
-      const result = statement.run();
-      console.log(`OK (${result.changes} changes)\n`);
-    }
-  } catch (err: any) {
-    console.error(`Error: ${err.message}\nDatabase: ${databasePath}`);
-    process.exitCode = 1;
-  } finally {
-    client?.close();
-  }
-}
-
-main();