Added better reporting for counts on all the indexers

[oblodgett]

No description provided.

[claude]

Code Review

This PR passes ProcessDisplayHelper as a parameter to the index() method and adds a new startProcess(long totalSize) overload so subclass indexers can report their total item count for progress tracking.

The changes look correct. This is a clean, mechanical refactor applied consistently across all indexer subclasses. A few observations:

1. Double startProcess is fine: The base class calls display.startProcess(className) (sets the message label), then subclasses call display.startProcess(totalSize) (sets the total count while preserving the message). Since no processing occurs between the two calls, the counter reset is harmless.

2. Inconsistent coverage: Some indexers (DatasetIndexer, DiseaseIndexer, GeneIndexer, GoIndexer, LiteratureIndexer, VariantIndexer, DiseaseAnnotationCurationIndexer, PhenotypeAnnotationCurationIndexer, ReleaseInfoIndexer, SiteMapAccessionCurationIndexer, GeneExpressionRibbonSummaryIndexer) accept the display parameter but never call display.startProcess(totalSize). This means they won't report total counts or show progress percentages/ETAs. This may be intentional (some don't have an easily available count), but worth confirming.

3. Redundant parameter: The display field is already inherited from the Indexer base class, so passing it as a method parameter is technically redundant — subclasses could access it directly. Not a problem, just a design note.

No bugs, no security concerns, no performance issues.