feat(issues): add typed metadata, comment, and dependency outputs

[SamMorrowDrums]

Summary

Migrate seven issue metadata, comment, dependency, and duplicate-detection tools to concrete NewTool[In, Out] DTOs. Modern protocol clients receive validated output schemas and structured content; legacy and unknown clients retain byte-exact text without structured output.

Why

Stacked directly on #3389 (sammorrowdrums-type-repository-tools) as the next bounded typed MCP migration layer. No issue is automatically closed.

What changed

• Type ListIssueTypes, ListIssueFields, AddIssueComment, UpdateIssueComment, IssueDependencyRead, IssueDependencyWrite, and FindDuplicate; retain API errors, scopes, feature gates, IFC labels, projections, and exported dependency-helper signatures.
• Preserve numeric-string coercions and optional-value presence at the compatibility boundary. Duplicate pagination retains API-owned defaults and explicitly supplied zeros; dependency pagination retains its existing defaults.
• Model single comment/reaction references and combined comment-plus-reaction results with an explicit closed union schema. The nullable zero union accommodates SDK error serialization and is removed from error wire results by the existing protocol middleware.
• Add modern/legacy/unknown tool-list and call contracts, exact text assertions, output-schema conformance, rejection of partial comment unions, and byte-exact REST/GraphQL API-error contracts. Update tool snapshots and protocol documentation.
• Keep ListIssues unchanged because it is already typed on the base. Defer the larger IssueRead, IssueWrite, and SubIssueWrite migrations to a separate layer, as agreed with the coordinator. Do not modify stack metadata.

MCP impact

• No tool or API changes
• Tool schema or behavior changed
  • Protocol 2026-07-28 and newer expose typed outputSchema and successful structuredContent for these seven tools; older/unknown protocols omit both. Errors omit structured content. Duplicate pagination schemas now permit explicit zero values to preserve existing handler behavior.
• New tool added

Prompts tested (tool changes only)

• Deterministic mocked MCP calls, not live GitHub prompts: list repository/organization issue types and single-select field definitions; add a comment, reaction, both, or a comment-targeted reaction; update a conversation comment.
• Deterministic mocked MCP calls: list blockers/blocking issues, add/remove blocked-by relationships with uppercase legacy inputs, find duplicates with omitted parameters or explicit zero pagination/threshold, and handle invalid inputs/API errors without structured success output.

Security / limits

• No security or limits impact
• Auth / permissions considered
  • Existing scope access and dependency/duplicate feature gates are unchanged; existing permission tests pass.
• Data exposure, filtering, or token/size limits considered
  • Existing minimal references, field definitions, repository visibility labels, and text shapes are preserved. No broader API payloads are exposed by structured output.

Tool renaming

• I am renaming tools as part of this PR (e.g. a part of a consolidation effort)
  • I have added the new tool aliases in deprecated_tool_aliases.go
• I am not renaming tools as part of this PR

Note: if you're renaming tools, you must add the tool aliases. For more information on how to do so, please refer to the official docs.

Lint & tests

• Linted locally with ./script/lint
  • script/lint — passed, 0 issues.
• Tested locally with ./script/test
  • script/test — passed, full go test -race ./... suite.
  • UPDATE_TOOLSNAPS=true go test ./... — passed; intentional issue snapshots updated.
  • script/generate-docs — passed; generated sections unchanged.
  • git diff --check — passed.
  • Live PAT-dependent e2e tests were not run; deterministic REST/GraphQL and protocol contract tests cover the migration.

Docs

• Not needed
• Updated (README / docs / examples)
  • README documents protocol-gated structured output for the migrated issue tools. Generated documentation was refreshed.