Flatten the repo: move everything out of app/ to the root

Now that the CLI and the Next.js app are one package, nesting it inside
app/ served no purpose - the repo root itself becomes the published
npm package. Merges app/.gitignore and app/README.md into the root
versions, drops the now-duplicate app/LICENSE, and updates path
references (README, docs/ARCHITECTURE.md, docs/CONFIG_REFERENCE.md,
package.json's repository.directory) that assumed the app/ nesting.

Also fixes a real bug this surfaced: the in-app docs viewer resolved
docs/ relative to process.cwd(), which only worked by accident when the
CLI happened to be invoked from app/'s parent directory. A first attempt
at fixing it with import.meta.dirname broke instead, for the same
cross-module-graph reason config-path resolution already documented -
Next compiles Route Handlers through a separate module graph that
doesn't preserve source-relative import.meta paths. Fixed by exposing
the app root via TRIGGERSHELL_APP_ROOT (set once in server.ts, where
import.meta *does* resolve correctly), the same pattern already used
for TRIGGERSHELL_CONFIG_PATH.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

src/cli/lib/env-file.ts

@@ -0,0 +1,43 @@
+import fs from "node:fs";
+
+interface EnvEntry {
+  key: string;
+  value: string;
+}
+
+function parseEnvLines(content: string): EnvEntry[] {
+  const entries: EnvEntry[] = [];
+  for (const line of content.split("\n")) {
+    const trimmed = line.trim();
+    if (!trimmed || trimmed.startsWith("#")) continue;
+    const eq = trimmed.indexOf("=");
+    if (eq === -1) continue;
+    entries.push({ key: trimmed.slice(0, eq), value: trimmed.slice(eq + 1) });
+  }
+  return entries;
+}
+
+/** Loads a `.env` file into `process.env`, without overriding vars already set. */
+export function loadDotenv(envPath: string): void {
+  if (!fs.existsSync(envPath)) return;
+  for (const { key, value } of parseEnvLines(fs.readFileSync(envPath, "utf-8"))) {
+    if (process.env[key] === undefined) process.env[key] = value;
+  }
+}
+
+/** Sets `key=value` in a `.env` file, replacing an existing line for that key rather than duplicating it. */
+export function upsertEnvVar(envPath: string, key: string, value: string): void {
+  const lines = fs.existsSync(envPath)
+    ? fs.readFileSync(envPath, "utf-8").split("\n")
+    : [];
+  const prefix = `${key}=`;
+  const index = lines.findIndex((line) => line.startsWith(prefix));
+  const newLine = `${key}=${value}`;
+  if (index >= 0) {
+    lines[index] = newLine;
+  } else {
+    if (lines.length > 0 && lines[lines.length - 1] === "") lines.pop();
+    lines.push(newLine);
+  }
+  fs.writeFileSync(envPath, lines.join("\n") + "\n");
+}