If a spec is written to yaml and then read back, it's dependencies do not correctly report .is_extension:

>>> from spack.spec import Spec
>>> x = Spec('git')
>>> x.concretize()
>>> y = Spec.from_dict(x.to_dict())
>>> y['libxml2'].package.is_extension
True
>>> x['libxml2'].package.is_extension
False

(Spec.to_yaml and Spec.from_yaml use the corresponding dict functions, so this affects specs that have been read from files).

Note that using Spec.copy() does not have this problem.

Two notes:

• Specs constructed with Spec.from_dict have _concrete set to False (although concrete is true if the original Spec was concrete)
• Package.is_extension refers to Spec._concrete

This suggests the following possible solutions:

• Package.is_extension uses Spec.concrete instead of Spec._concrete. This is done in Package.is_extension now uses Spec.concrete #3853 and has some (IMO valid) criticisms that the repercussions need to be clarified
• Spec.from_dict should set _concrete (perhaps if it doesn't change after concretization)
• Spec.to_dict should record whether the spec was concrete