Make docs file structure more docusaurus-friendly

[AHGIJMKLKKZNPJKQR]

Description

Now the generated docs have structure:

fishjam/
    index.md
    agents/
        index.md
    integrations/
        index.md
        gemini/

etc.

Motivation and Context

having the previous structure with fishjam.md and fishjam/ on the same level caused the autogenerated sidebar to duplicate entries.

Documentation impact

• Documentation update required
• Documentation updated in another PR
• No documentation update required

Types of changes

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to
  not work as expected)

[linear]

FCE-2517 Improve python server sdk docs generation

[Copilot]

Pull request overview

This PR restructures the documentation file organization to align with Docusaurus conventions by converting module documentation files into index files within their own directories.

Key changes:

• Updates the output path structure to create index.md files within module-specific directories instead of flat .md files
• Adjusts submodule link paths in templates to work with the new directory structure

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 1 comment.

File	Description
scripts.py	Changes output path from module.md to module/index.md format
templates/docusaurus/module.html.jinja2	Updates submodule links to use the new directory-based path structure

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[Copilot]

Pull request overview

Copilot reviewed 2 out of 2 changed files in this pull request and generated 1 comment.

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