docs: document embeddings limit overrides

[TuZaaaaa]

Summary

PR #1375 introduced support for:

• --embeddings 0 to disable the default node limit
• --embeddings to specify a custom node limit

These options are not currently documented in the README.

This PR adds:

• Documentation for embeddings limit overrides
• Usage examples
• Troubleshooting guidance for repositories exceeding the default 50,000-node safety cap

Motivation

Users working with large repositories may encounter skipped embeddings due to the default safety cap. The override options already exist, but are difficult to discover from the current documentation.

This change improves discoverability and reduces the need to search GitHub issues, pull requests, or Discord discussions.

[vercel]

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[magyargergo]

Nice one! Thanks for this change