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/configure.ts

@@ -0,0 +1,113 @@
+import * as p from "@clack/prompts";
+import pc from "picocolors";
+import { readConfig, writeConfig, configExists } from "../config/store.js";
+import type { PaperclipConfig } from "../config/schema.js";
+import { promptDatabase } from "../prompts/database.js";
+import { promptLlm } from "../prompts/llm.js";
+import { promptLogging } from "../prompts/logging.js";
+import { promptServer } from "../prompts/server.js";
+
+type Section = "llm" | "database" | "logging" | "server";
+
+const SECTION_LABELS: Record<Section, string> = {
+  llm: "LLM Provider",
+  database: "Database",
+  logging: "Logging",
+  server: "Server",
+};
+
+export async function configure(opts: {
+  config?: string;
+  section?: string;
+}): Promise<void> {
+  p.intro(pc.bgCyan(pc.black(" paperclip configure ")));
+
+  if (!configExists(opts.config)) {
+    p.log.error("No config file found. Run `paperclip onboard` first.");
+    p.outro("");
+    return;
+  }
+
+  const config = readConfig(opts.config);
+  if (!config) {
+    p.log.error("Could not read config file. Run `paperclip onboard` to recreate.");
+    p.outro("");
+    return;
+  }
+
+  let section: Section | undefined = opts.section as Section | undefined;
+
+  if (section && !SECTION_LABELS[section]) {
+    p.log.error(`Unknown section: ${section}. Choose from: ${Object.keys(SECTION_LABELS).join(", ")}`);
+    p.outro("");
+    return;
+  }
+
+  // Section selection loop
+  let continueLoop = true;
+  while (continueLoop) {
+    if (!section) {
+      const choice = await p.select({
+        message: "Which section do you want to configure?",
+        options: Object.entries(SECTION_LABELS).map(([value, label]) => ({
+          value: value as Section,
+          label,
+        })),
+      });
+
+      if (p.isCancel(choice)) {
+        p.cancel("Configuration cancelled.");
+        return;
+      }
+
+      section = choice;
+    }
+
+    p.log.step(pc.bold(SECTION_LABELS[section]));
+
+    switch (section) {
+      case "database":
+        config.database = await promptDatabase();
+        break;
+      case "llm": {
+        const llm = await promptLlm();
+        if (llm) {
+          config.llm = llm;
+        } else {
+          delete config.llm;
+        }
+        break;
+      }
+      case "logging":
+        config.logging = await promptLogging();
+        break;
+      case "server":
+        config.server = await promptServer();
+        break;
+    }
+
+    config.$meta.updatedAt = new Date().toISOString();
+    config.$meta.source = "configure";
+
+    writeConfig(config, opts.config);
+    p.log.success(`${SECTION_LABELS[section]} configuration updated.`);
+
+    // If section was provided via CLI flag, don't loop
+    if (opts.section) {
+      continueLoop = false;
+    } else {
+      const another = await p.confirm({
+        message: "Configure another section?",
+        initialValue: false,
+      });
+
+      if (p.isCancel(another) || !another) {
+        continueLoop = false;
+      } else {
+        section = undefined; // Reset to show picker again
+      }
+    }
+  }
+
+  p.outro("Configuration saved.");
+}