Changed: Update compose file to be run without decoder-eu script

See merge request !5

Changed: Removed port bindings

See merge request !4

Added: restart policy to each container

See merge request !3

Seperated user's preferences (configuration files) from user's data (MongoDB database and PKM Git root).
Moved the application files in standard directories ~/.config and ~/.local/share.

Added support for persistent MongoDB data and logs on docker volumes concretely in ~/.decoder-eu/mongodb/data and ~/.decoder-eu/mongodb/log.

Added missing dependencies (lima) in docker-compose.yaml, and removed dependency handling in app (useless).
Added 'select tools'.
Added geomety of CC UI in configuration files.

Added a mechanism for updating the user's preferences with user's confirmation of overwrite (and automatic backup in a .bak file).

Added support for configuring the Frama-C, Frama-Clang, ASFM, and Excavator services in the directory of the user's preferences.

Updated docker images location in docker-compose.yaml for Javaparser, Openjmlanalyzer, Classmodelxmi2jsontransformer, and Smmodelxmi2jsontransformer beacuse they have been moved to a new repository.

Variable Misuse API service added to docker compose

See merge request !2

Frontend config file

See merge request !1