[libcalamares] Partially fix implementation of timeout

- Adjust most call sites to use std::chrono::duration,
 - Call to QProcess::waitForFinished() needs work, since
   that takes milliseconds.

src/libcalamares/utils/CalamaresUtilsSystem.cpp

@@ -152,7 +152,7 @@ System::runCommand(
     const QStringList& args,
     const QString& workingPath,
     const QString& stdInput,
-    int timeoutSec )
+    std::chrono::seconds timeoutSec )
 {
     QString output;