Update docs generation to populate correct docs, remove redundant docs

[tommaso-moro]

Summary

This PR removes the redundant deprecated-tool-aliases.md as we already have tool-renaming.md and it also ensures that the autogeneration of docs populates the tool-renaming.md docs when generating the table for tool aliases

Tested locally

Why

Fixes duplicate docs issue

What changed

• Removed redundant docs
• Updated docs generation to populate the right docs (tool-renaming.md)

MCP impact

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

Prompts tested (tool changes only)

n/a

Security / limits

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

Lint & tests

• Linted locally with ./script/lint
• Tested locally with ./script/test

Docs

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

[Copilot]

Pull request overview

This PR consolidates documentation by removing the redundant docs/deprecated-tool-aliases.md file and updating the documentation generation system to populate the docs/tool-renaming.md file instead. The tool-renaming guide already contained all the relevant information about the deprecation alias system, making the separate deprecated-tool-aliases document unnecessary.

Key changes:

• Adds a "Current Deprecations" section to docs/tool-renaming.md with automated markers for auto-generation
• Deletes the redundant docs/deprecated-tool-aliases.md file completely
• Updates the docs generation configuration to target docs/tool-renaming.md instead of the deleted file

Reviewed changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated no comments.

File	Description
docs/tool-renaming.md	Adds "Current Deprecations" section with automated alias table markers to support auto-generation
docs/deprecated-tool-aliases.md	Removes redundant file - all content already covered in tool-renaming.md
cmd/github-mcp-server/generate_docs.go	Updates generateAllDocs to generate docs for tool-renaming.md instead of deprecated-tool-aliases.md

Note: While reviewing this PR, I noticed that README.md line 387 still references docs/deprecated-tool-aliases.md. This file is not part of the PR changes, but the link will be broken after this PR is merged and should be updated to point to docs/tool-renaming.md instead. Consider addressing this in a follow-up change or as part of running script/generate-docs after this PR is merged.