Increase the version to 1.2.5.1.

No real changes since 1.2.5, just fixed the date in the NEWS file and updating
the version to create a new tag.
Fix running gen_reference.py when building docs under Windows.

Python scripts need to be ran with shell=True, they can't be executed directly
by Python subprocess module as it tries to run them as Windows programs which,
unsurprisingly, fails.
Use relative path for antlr.jar to fix the build under Cygwin.

Make abspath function produces a Unix path under Cygwin which is not grokked
by Windows java.

Avoid the problem entirely by using relative paths.
Explicitly mark 2 gen_reference.py script as being Python 2.

This fixes its execution by sphinx-build on Windows machines with both Python 2
and Python 3 installed and shouldn't (hopefully) create problems elsewhere.
Fix antlr3 module path in PyInstaller config file.

Wrong path was (almost) silently ignored and antlr3 was simply not included in
the generated .exe file before, making it unusable.
Zip files quietly when making Windows distribution.

Listing all of the files (99% of which are Sphinx-generated HTML documentation)
is not useful.
Add explanations of how to make bakefile distribution.

Also remove the mention of submodules from the main README, the only currently
existing submodule (3rdparty/pyinstaller) is only needed for making bakefile
distributions under Windows, not using it.