🧹 config clean CLI command removes running manuscripts

[KagemniKarimu]

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Environment

📜 Manuscript Core:
  Version:	1.1.1

🏗️  Build Information:
  Go Version:	go1.21.3
  Rust Version:	1.83.0
  Git Commit:	ba24f01
  Built:	2024-12-30:16:13:55

💻 System Information:
  Unix Name:	Linux fedora-workstation 6.12.6-200.fc41.x86_64 #1 SMP PREEMPT_DYNAMIC Thu Dec 19 21:06:34 UTC 2024 x86_64 GNU/Linux
  OS/Arch:	linux/amd64

🐳 Docker Environment:
  Docker:	'27.4.1'

Steps to reproduce

1. run manuscript-cli init and create a manuscript
2. run manuscript-cli ls && manuscript-cli config show to verify manuscript was created
3. run manuscript-cli config clean and remove created manuscript while running

✔️ Expected Behavior

manuscript-cli should return an error when attempting to remove running manuscripts from config file (i.e. `ERROR: manuscript is currently running and must be stopped before being removed)

❌ Actual Behavior

manuscript-cli removes manuscript from config while manuscript is still running resulting in unexpected behavior (such as disappearing from the manuscript list and being unable to be stopped.