Updating README files.
New README files.
Updating main README file.
Small fixes in README files.
Makes '/bin' directory writable for busybox

If the '/bin' directory wasn't originally writable, that permission gets
restored by tarfile, and thus copying busybox in there will fail with
"Permission denied". We thus make sure it is writable when copying.
Merge branch 'v0.3' into 'fix-readonly-directories'

Conflicts:
	reprounzip/reprounzip/unpackers/default.py
Adds PyCharm's .idea folder to gitignore
Fixes a typo in installpkgs's help
Updates descriptions in the tool's helps
Adds --version
Fixes warnings from PyCharm
Rewrites reference to --use-chroot in vagrant help
Removes --pack option, now positional argument

Since the pack filename is required, having it be an option was useless.
However, it did make things more readable. Having "setup pack dir" and all
other commands "xxx dir" is clunky.
Adds a warning to NOT rm -rf a chroot

This only happens when mounting /dev and /proc ('setup/mount' or 'setup'
without '--dont-bind-magic-dirs').
"input_id"/"~_id" instead of "inputname"/"~name"
Details upload/download specifications everywhere

Previously, the help was only in vagrant's help message.
Rework "--no-" and "--dont-" flags

--no-use-chroot replaced by --dont-use-chroot (previous still works,
doesn't appear in help anymore)

--no-preserve-owner replaced by --dont-preserve-owner
Makes dir writable when uploading directory/chroot
Adds test for make_dir_writable()
Makes sure unittest2 is used