Move g:Profiler pair before GSEA/STRING; re-enable Day 1/2 parts

[hosseinvk]

Summary

• Restores g:Profiler (web) + gprofiler2 to immediately follow "Defining the gene list", ahead of GSEA/fgsea and STRING/STRINGdb: 08-1/08-2 -> 06-1/06-2 (gprofiler), 06-1/06-2 -> 07-1/07-2 (GSEA/fgsea), 07-1/07-2 -> 08-1/08-2 (STRING/STRINGdb). Pure renames, content unchanged except one stale cross-reference fixed ("earlier" -> "later in the book" in the gprofiler2-web chapter, since GSEA now comes after g:Profiler again).
• Updates make_R_script.R's chapter-exclusion list to match the new filenames.
• Reorders the Day 1 schedule on the overview page to follow suit (durations/instructors unchanged, just resequenced: g:Profiler -> GSEA -> STRING -> Reactome).
• Re-adds part-day1.Rmd/part-day2.Rmd into _bookdown.yml's rmd_files, matching the day split used in the schedule: Day 1 starts at the Recap chapter, Day 2 starts at clusterProfiler. Both are excluded from workshop.R generation like other non-code chapters.

Test plan

• Confirmed all 6 renames are content-identical apart from the one intentional wording fix.
• Full bookdown::render_book() completes cleanly with the new order.
• Confirmed the Day 1/Day 2 PART dividers render correctly in the sidebar TOC.
• Regenerated workshop.R and confirmed section order (gprofiler2 -> FGSEA -> STRINGdb -> ReactomePA -> clusterProfiler -> Novel species FEA) with no part-header leakage.
• CI bookdown-render job to be confirmed green before merge.