Slim down dependencies

[balhoff]

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[Copilot]

Pull request overview

This PR reduces transitive dependencies by replacing functionality previously provided by external libraries (owlet, owl-diff, robot-core, better-files, commons-codec, apache-jena-libs) with local implementations and narrower direct dependencies, while preserving behavior via new/updated tests.

Changes:

• Replaced Owlet-based SPARQL expansion with internal reasoner-backed VALUES expansion for anonymous variable ranges.
• Inlined lightweight utilities (Catalog XML IRI mapper, Markdown short forms, Manchester renderer, SHA-1 hashing) to remove heavy dependency trees.
• Swapped file I/O from better-files to java.nio, and narrowed Jena dependencies to jena-core + jena-arq.

Reviewed changes

Copilot reviewed 14 out of 15 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
src/main/scala/org/monarchinitiative/dosdp/SPARQL.scala	Adds reasoner-based expansion for anonymous class-expression ranges and warning behavior when no reasoner is provided.
src/main/scala/org/monarchinitiative/dosdp/cli/Query.scala	Removes Owlet query expansion and delegates reasoner-aware behavior into SPARQL.queryFor.
src/main/scala/org/monarchinitiative/dosdp/CatalogXmlIRIMapper.scala	Introduces a local catalog XML IRI mapper to replace robot-core usage.
src/main/scala/org/monarchinitiative/dosdp/MarkdownLinkShortFormProvider.scala	Adds a local Markdown link short form provider to replace owl-diff usage.
src/main/scala/org/monarchinitiative/dosdp/ManchesterSyntaxOWLObjectRenderer.scala	Adds a local Manchester renderer with local HTML escaping to replace owl-diff + commons-text transitive deps.
src/main/scala/org/monarchinitiative/dosdp/DOSDP.scala	Replaces commons-codec SHA-1 hex with JDK MessageDigest.
src/main/scala/org/monarchinitiative/dosdp/cli/Terms.scala	Replaces better-files output writing with java.nio.file.Files.write.
src/main/scala/org/monarchinitiative/dosdp/cli/Prototype.scala	Replaces better-files directory listing/extension logic with java.nio.file equivalents.
src/main/scala/org/monarchinitiative/dosdp/cli/Docs.scala	Updates imports to use the new local Markdown/Manchester rendering helpers.
src/main/scala/org/monarchinitiative/dosdp/Utilities.scala	Removes robot-core import and relies on the local catalog mapper.
src/test/scala/org/monarchinitiative/dosdp/QueryReasonerTest.scala	Adds tests for reasoner vs non-reasoner behavior for anonymous variable ranges.
src/test/scala/org/monarchinitiative/dosdp/MarkdownRenderingTest.scala	Adds tests for Markdown link rendering and literal escaping.
src/test/scala/org/monarchinitiative/dosdp/CatalogXmlIRIMapperTest.scala	Adds tests for local catalog mapper behavior (relative mapping, absolute mapping, DTD declaration).
src/test/scala/org/monarchinitiative/dosdp/GenerateDefinedClassTest.scala	Strengthens expectations around SHA-1 lowercase hex format.
build.sbt	Removes heavy deps and introduces narrower replacements (ELK artifact change, direct Jena modules, cats/circe version vars).

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