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/version.ts

@@ -0,0 +1,59 @@
+/**
+ * Version reporting — mode-aware.
+ *
+ * NPX mode:   the published package.json version (stamped by CI at release).
+ * Local mode: the git commit SHA of the checked-out clone (`git-<full-sha>`).
+ *             A clone has no meaningful semver, so the commit is the honest identifier.
+ */
+
+import { execFileSync } from 'node:child_process';
+import fs from 'node:fs';
+import path from 'node:path';
+import { fileURLToPath } from 'node:url';
+import { getMode } from './mode.js';
+
+const __dirname = path.dirname(fileURLToPath(import.meta.url));
+
+function readPackageVersion(): string {
+  try {
+    const pkgPath = path.join(__dirname, '..', 'package.json');
+    const pkg = JSON.parse(fs.readFileSync(pkgPath, 'utf-8')) as { version?: string };
+    return pkg.version || '1.0.0';
+  } catch {
+    return '1.0.0';
+  }
+}
+
+/** Run a git command in the CLI's own repo; returns trimmed stdout or null on any failure. */
+function git(...args: string[]): string | null {
+  try {
+    return execFileSync('git', args, { cwd: __dirname, encoding: 'utf-8', stdio: ['ignore', 'pipe', 'ignore'] }).trim();
+  } catch {
+    return null;
+  }
+}
+
+function readGitSha(): string | null {
+  return git('rev-parse', 'HEAD');
+}
+
+/**
+ * Version identifier. NPX: package.json version. Local: `git-<full-sha>`,
+ * falling back to the package version if git is unavailable.
+ */
+export function getVersion(): string {
+  if (getMode() !== 'local') return readPackageVersion();
+
+  const sha = readGitSha();
+  if (!sha) return readPackageVersion();
+
+  return `git-${sha}`;
+}
+
+/**
+ * Human-facing version line printed by `--version`.
+ * NPX: `shannon <version>`. Local: `shannon git-<full-sha>`.
+ */
+export function getVersionLine(): string {
+  return `shannon ${getVersion()}`;
+}