Before this commit, the startup file for a Python app got the standard
shebang `#!/usr/bin/env python` which is suitable for many projects but
not for Python 2 or 3 only packages. Now the shebang of the project's
main script of read and copied into the startup script.

Refactoring has broken the variable names -> fixed that

Before this commit, it was necessary to have a working installation of
`pandoc`. Now it is optional (but the long description is empty in that
case).

Added author, email, version, copyright and license to the `__init__.py`
of the top level package.

`--group` and `--hidden` flags are used now. If `group` is not
specified, `undefined` is used instead.

If the output file (given with `-o`) ends with `.dmg` the app is
automatically saved in an Apple Disk Image which can be used as a
distribution container and installer.

In previous versions, paths were joined by string operations. Now,
`os.path.join` is used instead which improves code readability and
platform independence.

The code used `encode` calls to write UTF-8 data to text files which is
not compatible with Python 3 text file mode. The code now uses the
`codecs` module which allows to write UTF-8 encoded text without code
changes in both Python 2 and 3.

- Reformatted code with `yapf` (120 characters line length)
- Do not use `format` for logging calls
- Added missing `__author__` statements

- App icon can be hidden
- Developer group can be configured
- Automatic graphics switching is supported by default

- New patch routine for the conda `activate` script
- Patch for the application path (conda saves an absolute path)

fixed in the package itself

Added patch routines for the conda gr package because it depends on
XQuartz; fixed library dependency errors for gks plugins and the main
libraries