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Improve flag handling
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 https://github.com/hiker/fab/issues/22