hadrian fails to re-generate dependencies when hs-boot files are modified

Steps to reproduce

1. Check out a clean master. (I was at b8e4fe23.)

2. Run hadrian/build _bootFileDeps/stage0/libraries/filepath/build/System/OsPath.o -o _bootFileDeps.

3. Add a silly import Data.ByteString.Builder () to libraries/filepath/System/OsPath.hs-boot.

4. Run the same command from step 2. This will fail with a message like the following:

   libraries/filepath/System/OsPath.hs-boot:5:1: error:
       Could not find module ‘Data.ByteString.Builder’
       There are files missing in the ‘bytestring-0.11.5.1’ package,
       try running 'ghc-pkg check'.
       Use -v (or `:set -v` in ghci) to see a list of the files searched for.
     |
   5 | import Data.ByteString.Builder ()
     | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

5. Delete _bootFileDeps/stage0/libraries/filepath/.dependencies.mk.

6. Run the same command from step 2. Now it succeeds again.

Expected behavior

Hadrian should not use stale .dependencies* information.