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Don't mark all packages as explicitly installed

postmarketOS Bot requested to merge fix/1212-all-depends-marked-as-explicitly-installed into master

Created by: ollieparanoid

pmbootstrap does dependency resolving on its own, and passes the list of resolved packages to apk when we want it to install something. The reason was outlined in #129:

fixing #120 (closed): packages do not get updated in "pmbootstrap install" after they have been rebuilt. For this to work, we specify all packages explicitly for abuild, instead of letting abuild do the resolving.

This new PR fixes #1212 (closed) (which noted that all of these dependencies were explicitly marked for installation) by doing the following:

  1. All packages and dependencies get attached to the virtual package .pmbootstrap instead of world
  2. We install the packages (without depends) explcitly
  3. .pmbootstrap gets removed, which means that all packages from 1. stay installed, but are no longer marked as explicitly installed. They will get removed automatically, when the depending packages get removed.

In addition, the mechanism for replacing the package of locally built packages with their full path, was broken and has been fixed in this commit. This is necessary to update packages of the same version with apk.

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