Kotaemon agnostic base

[Jesshuan]

Clean, folder archi, doc:

• 'rag system' README completed with all instructions
• split two distinct folders for the pipeline scripts
• restore all 'dev set-up' params for local agnostic dev
• remove specific database config within the code itself

Fix & improvements :

• Update Dockerfile for Kotaemon image building
• Fix Kotaemon bug : file_id filter during retrieval
• Ollama version fixed to 0.6.3 to prevent deep incompatibility with Kotaemon
• imporve ingestion versino system

[fraboniface]

LGTM, couldn't really test locally because I lack some credentials and GPU support but the changes make sense.

Tests still don't pass but I made some progress:

• Exclude .ipynb files from pre-commit Ruff analysis. The error message is now much more readable and we can see that all errors come from the policy analysis pipeline.
• Fixed some errors in kotaemon build (GHA and Dockerfile), but it still fails later in the process. I think it would need its own PR, and anyway we're likely to leave kotaemon altogether, so let's not dwell on this.

This is better than main, so I'll merge.