properly close OutStream and various fixes

[limwz01]

In order to support proper execution after resuming from an embedded kernel, we have to make sure that we can revert the IO alterations by the kernelapp using the close() method. The following fixes were made:

• Call close before embed returns
• Don't write the extra character on OutStream close() to pipe for watching thread if it's already dead or missing
• Add new variable closed so that "close" can be called multiple times without any error
• Don't use __stdout__ and __stderr__ at all
• Keep blackhole reference around so that the watching thread's pipe file descriptors do not get accidentally closed when the object is garbage collected (it happens now because it is not stored in __stdout__)
• Keep old IO variables and restore them when exiting
• More robust StreamHandler fixup and restore (but I think these should actually be completely removed)

[limwz01]

Fixes #1283

[limwz01]

I have no idea why the tests are failing and I currently do not have the appropriate python version to run the tests. But I'll work on it.