Improve consistency and reliability of tools in Stirling Engine

[jbrunton96]

Description of Changes

A few changes to improve things in the engine:

• Changed the PDF to Markdown code to be a real tool in Java, to remove the need for the pdf_ingest code, which looked a bit like an agent but wasn't behaving as an agent. It's now just covered automatically by the edit agent.
• Noticed that 0-parameter-endpoints were previously being ignored by the tool_models generator, so some tools which require no params were being mistakenly excluded.
• Removed tools which currently never succeed like Add Stamp, Cert Sign, and Overlay, because they require the supporting files to be sent in a different location in the API call, which we don't currently do. Ideally, we'd add proper support for this, but we're better off now removing support for these tools rather than just have them crash. We can re-add these tools in a future PR properly.

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