Add CLI package, config file support, and workspace setup

Add cli/ package with initial scaffolding. Add config-schema to shared
package for typed configuration. Add server config-file loader for
paperclip.config.ts support. Register cli in pnpm workspace. Add
.paperclip/ and .pnpm-store/ to gitignore. Minor Companies page fix.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

cli/src/commands/doctor.ts

@@ -0,0 +1,120 @@
+import * as p from "@clack/prompts";
+import pc from "picocolors";
+import { readConfig } from "../config/store.js";
+import {
+  configCheck,
+  databaseCheck,
+  llmCheck,
+  logCheck,
+  portCheck,
+  type CheckResult,
+} from "../checks/index.js";
+
+const STATUS_ICON = {
+  pass: pc.green("✓"),
+  warn: pc.yellow("!"),
+  fail: pc.red("✗"),
+} as const;
+
+export async function doctor(opts: {
+  config?: string;
+  repair?: boolean;
+  yes?: boolean;
+}): Promise<void> {
+  p.intro(pc.bgCyan(pc.black(" paperclip doctor ")));
+
+  const results: CheckResult[] = [];
+
+  // 1. Config check (must pass before others)
+  const cfgResult = configCheck(opts.config);
+  results.push(cfgResult);
+  printResult(cfgResult);
+
+  if (cfgResult.status === "fail") {
+    printSummary(results);
+    return;
+  }
+
+  const config = readConfig(opts.config)!;
+
+  // 2. Database check
+  const dbResult = await databaseCheck(config);
+  results.push(dbResult);
+  printResult(dbResult);
+  await maybeRepair(dbResult, opts);
+
+  // 3. LLM check
+  const llmResult = await llmCheck(config);
+  results.push(llmResult);
+  printResult(llmResult);
+
+  // 4. Log directory check
+  const logResult = logCheck(config);
+  results.push(logResult);
+  printResult(logResult);
+  await maybeRepair(logResult, opts);
+
+  // 5. Port check
+  const portResult = await portCheck(config);
+  results.push(portResult);
+  printResult(portResult);
+
+  // Summary
+  printSummary(results);
+}
+
+function printResult(result: CheckResult): void {
+  const icon = STATUS_ICON[result.status];
+  p.log.message(`${icon} ${pc.bold(result.name)}: ${result.message}`);
+  if (result.status !== "pass" && result.repairHint) {
+    p.log.message(`  ${pc.dim(result.repairHint)}`);
+  }
+}
+
+async function maybeRepair(
+  result: CheckResult,
+  opts: { repair?: boolean; yes?: boolean },
+): Promise<void> {
+  if (result.status === "pass" || !result.canRepair || !result.repair) return;
+  if (!opts.repair) return;
+
+  let shouldRepair = opts.yes;
+  if (!shouldRepair) {
+    const answer = await p.confirm({
+      message: `Repair "${result.name}"?`,
+      initialValue: true,
+    });
+    if (p.isCancel(answer)) return;
+    shouldRepair = answer;
+  }
+
+  if (shouldRepair) {
+    try {
+      await result.repair();
+      p.log.success(`Repaired: ${result.name}`);
+    } catch (err) {
+      p.log.error(`Repair failed: ${err instanceof Error ? err.message : String(err)}`);
+    }
+  }
+}
+
+function printSummary(results: CheckResult[]): void {
+  const passed = results.filter((r) => r.status === "pass").length;
+  const warned = results.filter((r) => r.status === "warn").length;
+  const failed = results.filter((r) => r.status === "fail").length;
+
+  const parts: string[] = [];
+  parts.push(pc.green(`${passed} passed`));
+  if (warned) parts.push(pc.yellow(`${warned} warnings`));
+  if (failed) parts.push(pc.red(`${failed} failed`));
+
+  p.note(parts.join(", "), "Summary");
+
+  if (failed > 0) {
+    p.outro(pc.red("Some checks failed. Fix the issues above and re-run doctor."));
+  } else if (warned > 0) {
+    p.outro(pc.yellow("All critical checks passed with some warnings."));
+  } else {
+    p.outro(pc.green("All checks passed!"));
+  }
+}