Hadrian: Fix untracked dependencies

This is a preparation for #16295: https://ghc.haskell.org/trac/ghc/ticket/16295

This commit mostly focuses on getting rid of untracked dependencies,
which prevent Shake's new `--shared` feature from appropriately caching
build rules.

There are three different solutions to untracked dependencies:

* Track them! This is the obvious and the best approach, but in some
  situations we cannot use it, for example, because a build rule creates
  files whose names are not known statically and hence cannot be
  specified as the rule's outputs.

* Use Shake's `produces` to record outputs dynamically, within the rule.

* Use Shake's `historyDisable` to disable caching for a particular build
  rule. We currently use this approach only for `ghc-pkg` which mutates
  the package database and the file `package.cache`.

These two tickets are fixed as the result:

Ticket #16271: ​https://ghc.haskell.org/trac/ghc/ticket/16271

Ticket #16272: ​https://ghc.haskell.org/trac/ghc/ticket/16272 (this one
is fixed only partially: we correctly record the dependency, but we
still copy files into the RTS build tree).

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