Move annotation start/end out of writers

[Wytamma]

I've moved the annotation start [ and end ] out of the writers so the writers won't break the newick spec.

[Copilot]

Pull Request Overview

This PR centralizes the annotation delimiters by moving the [ and ] wrappers out of the individual writer functions and into the newickRecurse function.

• In newickRecurse, annotation output is now wrapped with [ and ]
• beastAnnotation and nhxAnnotation no longer emit their own brackets

Comments suppressed due to low confidence (1)

src/io/writers/newick.ts:60

• [nitpick] After refactoring the annotation delimiters, add tests for nodes with and without annotations to verify that empty annotations do not produce [] and that valid annotations remain correctly formatted.

if (node.branchLength !== undefined) {

[Copilot]

Pull Request Overview

This PR moves the handling of annotation start/end markers out of individual annotation writers so that the writers no longer embed brackets and thereby break the spec.

• The newickRecurse function now extracts the annotation string and conditionally wraps it with brackets.
• The beastAnnotation and nhxAnnotation functions no longer prepend/append brackets, thus centralizing annotation formatting.

Comments suppressed due to low confidence (3)

src/io/writers/newick.ts:58

• Confirm that wrapping the annotation output with '[' and ']' in newickRecurse aligns with the intended specification, now that the writers only return the raw annotation content.

res += `[${annotation}]`;

src/io/writers/newick.ts:83

• Ensure documentation is updated to reflect that beastAnnotation no longer appends its own bracket wrappers, and now only returns the core annotation content for external wrapping.

res += '&';

src/io/writers/newick.ts:120

• Update documentation/comments for nhxAnnotation to indicate that it no longer handles its own closing bracket, and that the external caller is now responsible for adding the proper annotation delimiters.

res += '&&NHX:';

[LeoFeatherstone]

Thanks @Wytamma this is a vastly better solution!