Change thread shutdown again to also work with input framework.

Seems to work, tests pass, but not really verified.

Major change 1:
finished flag in MsgThread was replaced by 2 flags:
child_finished and main_finished.

child_finished is set by child_thread and means that the processing
loop is stopped immediately (no longer needed, no new input messages
will be processed, if loop continues running there is an ugly delay
on shutdown). (This took me a while to realize...)

main_finished is set by a message that is sent back by the child
to the main thread when Finished() is called (and child_finished
is set). when main_finished is set, processing of output messages
stops. But all messages that the child thread pushed in the queue
before calling Finish() are still processed.

Change 2:
Logging terminate call was replaced by a smaller call that just
flushes out the cache held by the main thread. This call
has to be done before thread shutdown is called - otherwhise
the threads will be shut down before all messages are pushed
on them. (This also took me a while to realize...).

Change 3:
Input framework actually calls it stop methods correctly (everything
was prepared, function call was missing)

src/threading/MsgThread.h

@@ -289,7 +289,8 @@ private:
 	 */
 	bool MightHaveOut() { return queue_out.MaybeReady(); }
 
-	/** Flags that the child process has finished processing. Called from child.
+	/** Sends a message to the main thread signaling that the child process
+	 *  has finished processing. Called from child.
 	 */
 	void Finished();
 
@@ -299,7 +300,8 @@ private:
 	uint64_t cnt_sent_in;	// Counts message sent to child.
 	uint64_t cnt_sent_out;	// Counts message sent by child.
 
-	bool finished;	// Set to true by Finished message.
+	bool main_finished;	// main thread is finished. Means child_finished propagated back through message queue.
+	bool child_finished;	// child thread is finished
 	bool failed;	// Set to true when a command failed.
 };