docs: remove duplicate tool listings and improve organization

[philip]

Remove 5 duplicate tool listings, move a few tools to more appropriate sections, and update a few descriptions.

[orca-security-us]

Orca Security Scan Summary

Status	Check	Issues by priority
Passed	Infrastructure as Code	0   0   0   0	View in Orca
Passed	SAST	0   0   0   0	View in Orca
Passed	Secrets	0   0   0   0	View in Orca
Passed	Vulnerabilities	0   0   0   0	View in Orca

[Copilot]

Pull Request Overview

This PR cleans up the README documentation by removing 5 duplicate tool listings that appeared multiple times across different sections, reorganizing tools into their appropriate categories, and improving tool descriptions for clarity.

Key changes:

• Removed duplicate entries for list_organizations, list_branch_computes, list_slow_queries, explain_sql_statement, prepare_query_tuning, and complete_query_tuning
• Moved list_organizations to the Project Management section where it belongs
• Consolidated query performance tools under a single "Query Performance Optimization" section
• Updated descriptions to be more consistent and removed overly specific implementation details

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[Copilot]

[nitpick] The updated description is now too generic. While removing specific mention of Stack Auth may be intentional to be provider-agnostic, 'an Auth provider' is vague. Consider specifying 'supported Auth providers' or linking to documentation that lists compatible providers to help users understand what authentication services can be integrated.

Suggested change

	- **`provision_neon_auth`**: Provisions Neon Auth for a Neon project. It allows developers to easily set up authentication infrastructure by creating an integration with an Auth provider.
	- **`provision_neon_auth`**: Provisions Neon Auth for a Neon project. It allows developers to easily set up authentication infrastructure by creating an integration with a supported Auth provider. See [Supported Auth Providers](https://docs.neon.tech/auth/providers) for a list of compatible authentication services.