`lib/fixup.rb` does not handle removing deprecated packages properly.

[Zopolis4]

Describe the bug When removing a deprecated package, lib/fixup.rb removes the files, but does not remove them from the list of installed packages. This is due to an error in the code for writing to device.json

To Reproduce Steps to reproduce the behavior:

1. Please indicate where the command(s) were executed.

satmandu/crewbuild:amd64 docker image (Digest: sha256:c650cf0911bd7b9f4cca4d3289386dbb1d9f68e2765e37958459338096d152a3

2. I executed the command(s) below:

     crew install js91
     crew update # Accept the removal of js91 here
     crew list installed | grep "js91"

   Output:

     chronos@67adfbd614ad /usr/local/lib/crew/packages $ crew update
     From https://github.com/chromebrew/chromebrew
      * branch                master     -> FETCH_HEAD
     HEAD is now at e62d1ce08 Vscodium 1.87.2.24072 => 1.89.1.24130 (#9780)
     Package lists, crew, and library updated.
   
     Js91 found in package fixup list
     Js91 is deprecated and should be removed.
     Js91: Replaced by newer versions of js.
   
     Would you like to remove deprecated package Js91? [y/N] y
     js91 removed!
     Checking for package updates...
     Your software is up to date.
   
     js91 # from the checking of crew list installed | grep "js91"

   Expected behavior That js91 is removed from the list of installed packages.

Expand

- Architecture: `x86_64` (`x86_64`) - Processor vendor: `GenuineIntel` - User space: `64-bit` - Chromebrew Kernel version: `5.10` - Chromebrew Running in Container: `true` - Chromebrew version: `1.48.1` - Chromebrew prefix: `/usr/local` - Chromebrew libdir: `/usr/local/lib64` - Last update in local repository: e62d1ce08 `Vscodium 1.87.2.24072 => 1.89.1.24130 (#9780) (33 minutes ago)` - OS variant: `Chrome OS` - OS version: `nocturne-release/R124-15823.40.0` - OS channel: `stable-channel`

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