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/lib/runner/registry.ts

@@ -0,0 +1,47 @@
+interface RunHandle {
+  runId: string;
+  scriptId: string;
+  controller: AbortController;
+  pid?: number;
+}
+
+declare global {
+  var __triggershellRunHandles: Map<string, RunHandle> | undefined;
+}
+
+/** In-memory only - live run handles cannot survive a process restart; see `reconcileOrphanedRuns`.
+ * Anchored on `globalThis` - see the comment in `runner/events.ts` for why a plain module-level
+ * singleton isn't safe here (Next compiles Route Handlers through a separate module graph from
+ * what `server.ts` requires directly). */
+const handles: Map<string, RunHandle> = globalThis.__triggershellRunHandles ?? new Map();
+globalThis.__triggershellRunHandles = handles;
+
+export function registerRun(handle: RunHandle) {
+  handles.set(handle.runId, handle);
+}
+
+export function unregisterRun(runId: string) {
+  handles.delete(runId);
+}
+
+export function getRunHandle(runId: string): RunHandle | undefined {
+  return handles.get(runId);
+}
+
+export function isRunLive(runId: string): boolean {
+  return handles.has(runId);
+}
+
+/** Requests cancellation; returns false if the run isn't tracked (already finished or not this process). */
+export function cancelRun(runId: string): boolean {
+  const handle = handles.get(runId);
+  if (!handle) return false;
+  handle.controller.abort();
+  return true;
+}
+
+export function killAllRuns() {
+  for (const handle of handles.values()) {
+    handle.controller.abort();
+  }
+}