Added marker and xml as ODE extraction options

[rush17m]

This PR adds Marker as a second PDF extraction method, an XML equation extraction method as well as supporting changes for cleaner organization of downloaded and extracted content.

Changes

1. New PDF extractor: marker

   • Users can now choose between marker and mineru when running the PDF extraction pipeline to obtain ODEs.

2. Bulk template model generation script

   • Extraction parameters are now easier to configure.
   • Improved handling of output storage to keep extracted files and generated content organized.

3. New extraction method: XML

   • Added support for generating ODEs directly from XML files from PubMed.
   • The extraction method option now accepts three values: mineru, marker, and xml.