Docs: document reconciled isa-miappe-combined v0.2 profile

[sorenwacker]

Documentation task. Document the reconciled isa-miappe-combined v0.2 profile. Proposed: a profiles page (e.g. docs/profiles/isa-miappe-combined.md) linked under the Profiles nav, plus a short entry in CHANGELOG.md.

What to document

• Purpose: ISA framework extended with MIAPPE 1.2 plant-phenotyping entities; a single normalized profile intended as the source of truth for downstream SEEK export (see the SEEK export docs task).
• Reconciliation vs v0.1 (v0.1 is retained). v0.2 removes redundant/ambiguous modeling:
  • single unique_id key (dropped identifier everywhere; references repointed to *.unique_id);
  • single factor model Factor + FactorValue (dropped StudyFactor, Factor.values, FactorValue.factor_name; FactorValue.value now required; FactorValue.factor_id references Factor.unique_id);
  • experimental-site geolocation on Study (dropped the redundant Location entity);
  • germplasm material source inline on BiologicalMaterial (dropped the redundant MaterialSource entity).
  • 27 entities (was 30), 55 validation rules (was 57). Root entity Investigation.
• MIAPPE 1.2 alignment: entity-complete against MIAPPE 1.2; carries the 1.2 trait-decomposition and expanded material-source fields.
• How it was built: via the spec-builder MCP tools (spec_clone 0.1 -> spec_delete_entity/spec_delete_field/spec_update_field/spec_delete_rule/spec_update_rule -> spec_set_metadata -> spec_validate -> spec_save). spec_validate returns clean.

Note

Keep the page free of duplicated content already covered by the ISA and MIAPPE profile pages; cross-reference them instead.

[sorenwacker]

Draft of the reconciled isa-miappe-combined v0.2 profile lives in commit f8f0f8e (was on branch dcat-docs-seek-combined, now deleted as part of branch cleanup). Recover with git show f8f0f8e / git checkout f8f0f8e -- <path> if this issue is picked up.