feat(pkgctl): add internal update checksums to better control output

This allows us to have more control over the output and status logs.
Using this method we are able to avoid cluttering the version upgrade
subcommand while downloading sources for updating the checksums.

Having this internally will also allow us in the future to have smart
checksums updating by only trying to change the checksums of sources
that have actually changed, for example when adjusting a patch file we
should avoid trying to overwrite the archive checksums unintentionally.

Component: pkgctl version upgrade

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