@startuml

package "Facade System (Host Scripts)" {
  [run_knockouts.py]
  [run.cmd / bat / sh] as run_script
  [stop.cmd / bat / sh] as stop_script
  [master_openworm.py]
  [mutant_sibernetic.py]
  [movement_analysator.py]
  [compile_report.py]
}

node "OpenWorm Container" {
  [sibernetic.py]
  [Simulation Engine]
}

database "File System" {
  [knockout_progress.json]
  [final.pdf]
}

' Pipeline Execution Flow
[run_knockouts.py] --> run_script : 1. executes (-fname)
run_script --> [master_openworm.py] : calls
run_script --> [Simulation Engine] : starts container
[run_knockouts.py] --> stop_script : 3. executes post-sim
stop_script --> [Simulation Engine] : stops container
[run_knockouts.py] --> [movement_analysator.py] : 4. executes analysis

' Code Patching and Overrides
[run_knockouts.py] --> [mutant_sibernetic.py] : patches kwargs (Python)
[master_openworm.py] --> [mutant_sibernetic.py] : extracts / prepares
[mutant_sibernetic.py] --> [sibernetic.py] : overrides in container

' Data & State Management
[run_knockouts.py] --> [knockout_progress.json] : reads / saves state
[movement_analysator.py] --> [knockout_analysis_report.tex] : generates .tex segments
[compile_report.py] --> [final.pdf] : compiles master report

note right of [run_knockouts.py]
  Pipeline controller:
  Loops through scenarios,
  sets env variables, and
  compiles LaTeX results.
end note

@enduml