Replace ml-paper-writing with research-paper-writing: full research pipeline skill

Replaces the writing-focused ml-paper-writing skill (940 lines) with a
complete end-to-end research paper pipeline (1,599 lines SKILL.md + 3,184
lines across 7 reference files).

New content:
- Full 8-phase pipeline: project setup, literature review, experiment
  design, execution/monitoring, analysis, paper drafting, review/revision,
  submission preparation
- Iterative refinement strategy guide from autoreason research (when to use
  autoreason vs critique-and-revise vs single-pass, model selection)
- Hermes agent integration: delegate_task parallel drafting, cronjob
  monitoring, memory/todo state management, skill composition
- Professional LaTeX tooling: microtype, siunitx, TikZ diagram patterns,
  algorithm2e, subcaption, latexdiff, SciencePlots
- Human evaluation design: annotation protocols, inter-annotator agreement,
  crowdsourcing platforms
- Title, Figure 1, conclusion, appendix strategy, page budget management
- Anonymization checklist, rebuttal writing, camera-ready preparation
- AAAI and COLM venue coverage (checklists, reviewer guidelines)

Preserved from ml-paper-writing:
- All writing philosophy (Nanda, Farquhar, Gopen & Swan, Lipton, Perez)
- Citation verification workflow (5-step mandatory process)
- All 6 conference templates (NeurIPS, ICML, ICLR, ACL, AAAI, COLM)
- Conference requirements, format conversion workflow
- Proactivity/collaboration guidance

Bug fixes in inherited reference files:
- BibLaTeX recommendation now correctly says natbib for conferences
- Bare except clauses fixed to except Exception
- Jinja2 template tags removed from citation-workflow.md
- Stale date caveats added to reviewer-guidelines.md

skills/research/research-paper-writing/templates/neurips2025/Makefile

@@ -0,0 +1,36 @@
+FIGURES_FOLDER := figures
+PDFS := \
+$(filter-out $(wildcard $(FIGURES_FOLDER)/*-crop.pdf),$(wildcard $(FIGURES_FOLDER)/*.pdf)) \
+$(filter-out $(wildcard $(FIGURES_FOLDER)/**/*-crop.pdf),$(wildcard $(FIGURES_FOLDER)/**/*.pdf))
+CROPPED_PDFS := $(PDFS:.pdf=-crop.pdf)
+
+all: main.pdf
+
+%.pdf: %.tex Makefile $(CROPPED_PDFS)
+	pdflatex -synctex=1 -interaction=nonstopmode $<
+	-bibtex $*.aux
+	pdflatex -synctex=1 -interaction=nonstopmode $<
+	pdflatex -synctex=1 -interaction=nonstopmode $<
+
+.PHONY: figures
+figures: $(CROPPED_PDFS)
+
+.PRECIOUS: $(CROPPED_PDFS)
+%-crop.pdf: %.pdf Makefile
+	pdfcrop $<
+
+.PHONY: clean upgrade
+clean:
+	find . -maxdepth 1 \
+		\( -name "*.aux" -o -name "*.bbl" -o -name "*.blg" -o \
+	           -name "*.log" -o -name "*.out" -o -name "*.pdf" -o \
+		   -name "*.synctex.gz" \) | xargs $(RM)
+	find $(FIGURES_FOLDER) -name "*-crop.pdf" | xargs $(RM)
+
+YEAR := 2025
+
+upgrade:
+	curl -O https://media.neurips.cc/Conferences/NeurIPS$(YEAR)/Styles.zip
+	unzip -u Styles.zip
+	mv Styles/neurips_${YEAR}.sty neurips.sty
+	$(RM) -r Styles.zip Styles