Relocation for analyzed flags & paper modifications#18
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Added functionality to set the `analyzed` and `adjoint_analyzed` flags within the `analyze` and `analyze_adjoint` methods directly. Now, users do not have to set these flags within their private/protected methods (although they still can without causing issues).
Reflects the change made to Analysis base class, which now sets the flags for `analyzed` and `adjoint_analyzed` directly within the base class during execution.
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Modified the location where the
analyzedandadjoint_analyzedboolean flags are set for the Analysis base class to eliminate the need for a user to include them when creating subclasses. Also, various modifications for the JOSS paper prior to submission.