Improve flag handling

[hiker]

ATM (and with #311) coming in, there is no consistent way of handling flags - some were added in #311 which do not allow path-specific flags (mostly to keep the PR reasonable small). Some issues that need to be fixed:

• Have just one flag object for every tool flag
• Support adding and removing flags
• Potentially use a dict to allow O(1) removal of flags (be careful that ordering of flags might be important)
• Have flags depend on compiler version

Note that this issue is also covered in hiker/fab#22