Fix myst cross-reference warnings. Also fix TOC.

[espenhgn]

** The documentation issue**
There are now some myst cross-reference issues between files occurring with the online docs build using sphinx:

cd sphinx-docs/source
make html
....
preparing documents... done
writing output... [100%] usecases/saige_demo                                                                                                                                                  
/Users/espehage/Repositories/containers/docs/README.md:9: WARNING: 'myst' cross-reference target not found: './specifications/README.md' [myst.xref_missing]
/Users/espehage/Repositories/containers/docker/README.md:7: WARNING: 'myst' cross-reference target not found: './../docs/singularity/hello.md' [myst.xref_missing]
/Users/espehage/Repositories/containers/docker/README.md:9: WARNING: 'myst' cross-reference target not found: './../CONTRIBUTING.md' [myst.xref_missing]
/Users/espehage/Repositories/containers/docker/README.md:11: WARNING: 'myst' cross-reference target not found: './../usecases/gwas_demo.md' [myst.xref_missing]
/Users/espehage/Repositories/containers/docker/README.md:15: WARNING: 'myst' cross-reference target not found: './../usecases/README.md' [myst.xref_missing]
/Users/espehage/Repositories/containers/docker/README.md:28: WARNING: 'myst' cross-reference target not found: './../docs/singularity/README.md' [myst.xref_missing]
/Users/espehage/Repositories/containers/docker/README.md:32: WARNING: 'myst' cross-reference target not found: './../README.md' [myst.xref_missing]
/Users/espehage/Repositories/containers/scripts/README.md:5: WARNING: 'myst' cross-reference target not found: './gwas/README.md' [myst.xref_missing]
/Users/espehage/Repositories/containers/scripts/README.md:6: WARNING: 'myst' cross-reference target not found: './pgs/README.md' [myst.xref_missing]
/Users/espehage/Repositories/containers/usecases/README.md:5: WARNING: 'myst' cross-reference target not found: './gwas_demo.md' [myst.xref_missing]
/Users/espehage/Repositories/containers/usecases/README.md:5: WARNING: 'myst' cross-reference target not found: './../docs/specifications/README.md' [myst.xref_missing]
/Users/espehage/Repositories/containers/usecases/README.md:6: WARNING: 'myst' cross-reference target not found: './gwas_real.md' [myst.xref_missing]
/Users/espehage/Repositories/containers/usecases/README.md:7: WARNING: 'myst' cross-reference target not found: './meta_simu.md' [myst.xref_missing]
/Users/espehage/Repositories/containers/usecases/README.md:8: WARNING: 'myst' cross-reference target not found: './bolt-lmm_demo.md' [myst.xref_missing]
/Users/espehage/Repositories/containers/usecases/README.md:9: WARNING: 'myst' cross-reference target not found: './saige_demo.md' [myst.xref_missing]
/Users/espehage/Repositories/containers/usecases/README.md:10: WARNING: 'myst' cross-reference target not found: './../scripts/pgs/LDpred2/README.md' [myst.xref_missing]
generating indices... genindex done
writing additional pages... search done
...

Adding a proper hierarchy for the table of contents would be good.

[github-actions]

This issue appears to be stale due to non-activity