feat(cli): restructure run folder and improve terminal UX (#384)

* feat: surface report at run root and nest run internals under .shannon

* feat: use plain-language wording in user-facing terminal messages

* feat(cli): guide users to watch scan progress and surface report path on start

* docs: sync run-folder layout and CLI wording across docs and comments

* feat(cli): add version command reporting package version or git SHA

* feat(cli): detect TTY for interactive prompts, color, and progress output

* docs: document --yes flag, version command, and tty module

* fix(cli): FORCE_COLOR precedence and plain uninstall --yes output

* fix(cli): respect empty NO_COLOR

* fix(cli): let NO_COLOR take precedence over FORCE_COLOR

* docs: mark claude-code-router integration as removed

apps/cli/src/tty.ts

@@ -0,0 +1,34 @@
+/**
+ * Terminal capability detection — output coloring, cursor animation, and
+ * whether the user can be prompted interactively.
+ */
+
+/** True when stdout is a real terminal — safe for color, cursor moves, and spinners. */
+export function stdoutIsTerminal(): boolean {
+  return !!process.stdout.isTTY;
+}
+
+/** True when both stdin and stdout are terminals, so interactive prompts can run. */
+function isInteractive(): boolean {
+  return !!process.stdin.isTTY && !!process.stdout.isTTY;
+}
+
+/** True when color escapes should be emitted. NO_COLOR disables; FORCE_COLOR overrides (0/false/empty = off). */
+export function supportsColor(): boolean {
+  if (process.env.NO_COLOR !== undefined) return false;
+
+  const force = process.env.FORCE_COLOR;
+  if (force !== undefined) {
+    return force !== '0' && force !== 'false' && force !== '';
+  }
+
+  return stdoutIsTerminal();
+}
+
+/** Exit with a clear error when an interactive-only command has no terminal, instead of hanging on a prompt. */
+export function requireInteractive(command: string, alternative: string): void {
+  if (isInteractive()) return;
+  console.error(`ERROR: '${command}' needs an interactive terminal.`);
+  console.error(alternative);
+  process.exit(1);
+}