pkg/declextract: move file update from pkg/clangtool

Currently when entities are added/changed, one may need to update
both pkg/declextract and pkg/clangtool b/c clangtool updates paths.
Move all of that updates to pkg/declextract, so that pkg/clangtool
does not need to be touched when entities change.
The idea behind pkg/clangtool is to provide lower-level infrastructure
function of running the clang tool only.

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