Sync all Jupyter notebooks from freiburgermsu fork

[freiburgermsu]

Summary

Single PR carrying every .ipynb path that differs from the freiburgermsu fork (synced to freiburgermsu/ModelSEEDpy@971df5d main): 36 added, 35 updated, 4 removed, 19 moved. The changes fall into four groups:

1. Sphinx/ReadTheDocs integration: new docs/source/{escher,flux_analysis,kbase,model_reconstruction,others}/ notebook trees, which are byte-identical mirrors of the corresponding examples/ notebooks; many examples gained a markdown H1 title cell for nbsphinx, and the Index.ipynb files were trimmed. Companion to the .rst docs PR Sync all .rst documentation files from freiburgermsu fork #73.
2. examples/ reorganization: Community Modeling/ restructured into MSSteadyCom/ and Thermo/ subdirectories (the old MSCommunity/ folder is dissolved into MSSteadyCom/); Flux Analysis/ gained Thermo/ and dFBA/ subdirectories.
3. New notebooks: minimal media (examples/minimal_media.ipynb, examples/minimal_media/troubleshooting.ipynb), HTML_report.ipynb, correcting_templates.ipynb, CustomBuilder.ipynb, simulate_nb.ipynb, and a community-modeling set (build_community_model*.ipynb, network_diagram.ipynb, dFBA comparison.ipynb).
4. Content updates: of the 35 modified notebooks, 19 have real source edits (notably MSCompatibility.ipynb doubled with SMETANA testing sections, build_metabolic_model.ipynb switched to the newer MSBuilder API, Genomes.ipynb gained MSGenome.from_fasta cells); the other 16 are only re-run outputs/metadata.

Caveats

• The community-modeling notebooks exercise modelseedpy/community/, which Remove the community subpackage and its tests #31 removes (and MSCompatibility.ipynb %runs two module files that no longer exist in either fork) — you may prefer to drop those notebooks; happy to adjust.
• Included for faithfulness are five duplicate artifacts from the reorganization (*.ipynb copy ×4 and MSCommunity_thermo-Copy1.ipynb) — say the word and I'll drop them from this PR.
• Notebook plots reference sibling image/CSV files not included here (available as a follow-up PR if wanted).

🤖 Generated with Claude Code

https://claude.ai/code/session_017rcBA87xipNeaukuFW8N2G