Add rationale and confidence to closing an issue

[iulia-b]

• closes https://github.com/github/plan-track-agentic-toolkit/issues/343

Summary

Similar to fields and type, this PR adds the ability of suggesting a "close issue" intent, with confidence, rationale, and support for duplicate issue .

Why

Fixes https://github.com/github/plan-track-agentic-toolkit/issues/343

What changed

• Rewrote the granular update_issue_state tool as a standalone function (off the issueUpdateTool helper)
• added four new optional params: rationale, confidence, is_suggestion, and duplicate_of
• When intent params are provided, the tool sends the state as an object {"state": {"value": "closed", ...}} to the REST API instead of a plain string
• duplicate_of accepts an issue number and resolves it to a DB id before sending duplicate_issue_id in the request body.
• Suggestion closes as duplicate require duplicate_of. Direct closes do not.

MCP impact

• No tool or API changes
• Tool schema or behavior changed
• New tool added

Prompts tested (tool changes only)

Security / limits

• No security or limits impact
• Auth / permissions considered
• Data exposure, filtering, or token/size limits considered

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
• Tested locally with ./script/test

Docs

• Not needed
• Updated (README / docs / examples)