Commandline prepare phase overwrites plan defined prepare phases (expected) but it keeps the number of phases

[tcornell-bus]

Reproducer:

tcornell /tmp/tmt-testing $ cat plan.fmf 
discover:
    how: fmf
execute:
    how: tmt
adjust+:
  - when: distro == fedora-42
    prepare+:
      - name: thing 1
        how: shell
        script: echo "thing 1"
      - name: thing 2
        how: shell
        script: echo "thing 2"
tcornell /tmp/tmt-testing $ cat test.fmf 
test: /bin/true
tcornell /tmp/tmt-testing $ tmt --context distro=fedora-42 run -a provision -h container -i fedora:42 prepare --how install --package procps-ng
[...]
   prepare
        queued push tasks
            #1: push to default-0
        
        push task #1: push to default-0
    
        queued prepare tasks
            #1: essential-requires on default-0
            #2: thing 1 on default-0
            #3: thing 2 on default-0
        
        prepare task #1: essential-requires on default-0
        how: install
        summary: Install essential required packages
        name: essential-requires
        where: default-0
        package: /usr/bin/flock
        
        prepare task #2: thing 1 on default-0
        how: install
        name: thing 1
        package: procps-ng
        
        prepare task #3: thing 2 on default-0
        how: install
        name: thing 2
        package: procps-ng
    
        queued pull tasks
            #1: pull from default-0
        
        pull task #1: pull from default-0
    
        summary: 3 preparations applied

I expected it to overwrite the plan defined prepare phases with a single install phase, but it overwrote and performed two install phases. Low priority as it doesn't break anything, but weird.

Possibly related to #4761

[thrix]

From triage meeting:

• long term (kinda known) issue with tmt
• the root cause is that we do not have a remove of phases in tmt
• the triagers agree it does not feel natural, and should be fixed