feat(trees): add tree repair utility

[grantfitzsimmons]

Integrates fixes requested in #7307, reimplemented since it has been too long since the original PR

Fixes #7138

This PR introduces changes that add new tree repair options, including support for rebuilding full names for all nodes in a tree, both excluding and including synonyms. Descriptions of each function have been added under a new "Tree Options" menu. It also adds a nice wrench icon more fitting for the repair tree tool.

newTreeOptions.mp4

treeDemoGitHub.mp4

This has its own permission, so if the user doesn't have the rebuild_full_names for a particular tree, every option will be hidden except for the repair tree option (which has its own permission).

Checklist

• Self-review the PR after opening it to make sure the changes look good and
  self-explanatory (or properly documented)
• Add relevant issue to release milestone
• Add pr to documentation list
• Add automated tests
• Add a reverse migration if a migration is present in the PR

Testing instructions

In progress... 🚧

Rebuild Full Names

There is a new option to recompute and update the fullName field for all nodes in a chosen tree definition (Taxon, Geography, Storage, TectonicUnit, GeologicTimePeriod, LithoStrat). It only touches rows whose stored value is missing or differs from the recalculated value.

API endpoint:
/api/specify_tree/{tree}/{treedef_id}/rebuild-full-name

Optional parameter: ?rebuild_synonyms=true (also updates synonym nodes; default is accepted/preferred nodes only as when updating a tree definition)

Examples:
Accepted only: /api/specify_tree/taxon/2/rebuild_fullname
Accepted + synonyms: /api/specify_tree/geography/4/rebuild_fullname?rebuild_synonyms=true

Response (example):

{
  "success": true,
  "rebuild_synonyms": true,
  "changed": { "accepted": 95, "synonyms": 25, "total": 120 }
}

Permissions:
User must have rebuild_fullname on /tree/edit/{tree}. If missing, expect 403.

When to test:

• After editing rank definition items (separators, direction, before/after text) where synonyms were not automatically updated.
• After bulk fullName edits via SQL.
• After tree operations that would otherwise not update synonyms.

Note

You will likely need to edit node fullName values using SQL to test this effectively. In testing, I used an approach like this one on different trees:

select TaxonID, Name, FullName, isAccepted, TaxonTreeDefID from taxon
where TaxonTreeDefID = 17
order by isAccepted asc;

This let me update a mix of both synonyms and accepted names to verify counts are appropriate and that only the specified tree is updated.

UI testing:

1. Open the Repair Tree menu from User Tools
2. Click the ⚙️ (options button) next to the tree definition pencil.
3. Choose both rebuild options
4. A small status message shows how many names were updated or that none changed.

What to verify:

• Counts in response look reasonable (non-zero if you deliberately changed inputs).
• Synonym rebuild only increments synonyms when ?rebuild_synonyms=true (when using the appropriate button).
• No change to node relationships or ranks.
• Re-running immediately yields zero changes (no names should need an update).

Difference from existing “Repair Tree” function:
Repair fixes structural numbering; rebuild_fullname only recalculates display names.