refactor: convert Software.md into a Software/ directory for better organization

[benjibromberg]

Context

In PR #2 review, @jplotts noted that Software.md could be better organized (thread). The file has grown to 52 entries across 6 H2 sections, with three sections carrying 11–16 entries each (Metabolic Modeling & Strain Design, Mass Spectrometry & Chemometrics, AI Agents & Foundation Models).

Proposal

Convert Software.md into a Software/ directory, mirroring the existing ResearchAreas/ pattern:

Software.md                    # Becomes a landing page / TOC
Software/
  MetabolicModeling.md         # 11 entries → sub-grouped by H2
  MassSpectrometry.md          # 14 entries → sub-grouped (feature detection / annotation / stats)
  AIAgents.md                  # 16 entries → sub-grouped (foundation models / agents / benchmarks)
  ...                          # one file per current H2 section

Each per-category file keeps the existing "H2 = sub-area, H3 = tool" schema — no schema change. Sub-categorization happens naturally as H2s within each file, which is exactly what Jim's comment was asking for.

Decisions to surface

• Same treatment for Data.md? It's also growing long and would benefit from the same split — worth deciding in lockstep so the repo stays internally consistent.
• Cross-category tools (e.g. a metabolic-modeling tool that's also an AI agent) — primary home + cross-link, or duplicate the entry?
• Schema docs: CLAUDE.md and CONTRIBUTING.md currently describe the single-file Software.md layout; both need updates as part of the refactor.

Acceptance

• Software/ directory created with one file per current H2 category
• Root Software.md becomes a short TOC landing page linking to each category
• Long sections (Metabolic Modeling, Mass Spec, AI Agents) sub-grouped via H2s within their per-category file
• CLAUDE.md + CONTRIBUTING.md updated to document the new layout
• Any cross-links pointing into Software.md (e.g. from ResearchAreas/AITooling.md "Related Software" sections) updated to the new paths

Sequencing

PR #2 is approved and should land as-is — this refactor is a follow-up PR off main once #2 merges.