Refactoring of pdf_extract.py script

[AdevGarcia]

Description:
This PR refactors the pdf_extract.py script to improve readability and maintainability of the code.
In order not to affect the current code, the app.py script and the app_tools library have been created.
app.py performs the same process as pdf_extract.py.
The app_tools library incorporates the refactorings of the different steps.

app_tools
|- pdf.py
|- layout_analysis.py
|- formula_analysis.py
|- ocr_analysis.py
|- table_analysis.py
|- visualize.py
|- config.py
|- utils.py

If you find it interesting you can replace app.py with pdf_extract.py

Motivation:
I love the project, I would like to thank you for the great work done.
Refactoring is done to continue working to create an api with fastAPI and Docker.

Main changes:

• The script app.py has been created with the pipeline of pdf_extract.py.
• The library app_tools has been created that contains the classes and methods to perform each step of the pipeline.
• pdf.py: Provides a set of app_tools for working with PDF files.
• layout_analysis.py: Analyzes the layout of documents by detecting the layout of each page in a document image.
• formula_analysis.py: Is designed to handle formula detection and recognition in images.
• ocr_analysis.py: OCR Processor. It is responsible for performing OCR recognition.
• table_analysis.py: Represents a Table Processor that is used for table recognition in documents.
• visualize.py: It generates visualizations of the document layout
• config.py: Configure model parameters and logs
• utils.py: save results in json

Functionality impact: No change to existing functionality is expected, as the refactoring does not introduce new features or modify existing ones.

Instructions for Reviewers:

• Review the app.py and app_tools scripts to ensure that the logic has been ported correctly.
• Verifies that there are no observable changes in the system's behavior when running the tests.

Example of Use:

python app.py --pdf 1706.03762.pdf