fix(think): warn when skills hide system prompt fallback

[cjol]

This PR documents getSystemPrompt() as a fallback-only API and adds a warning for the confusing getSystemPrompt() plus getSkills() combination. Addresses #1871.

Why

• getSkills() registers the skills catalog as a Session context block, so Think correctly treats getSystemPrompt() as fallback-only once skills are present.
• That behavior is easy to miss because an agent can override both APIs and still run, but its getSystemPrompt() instructions will not reach the model.
• We could merge getSystemPrompt() with context blocks, but that changes behavior for existing agents that use Session context as the system prompt source.
• The safer path is to keep the current prompt assembly semantics, document them clearly, and warn when a likely footgun is detected.

Code Changes

• Updates getSystemPrompt() JSDoc and the Think README to describe it as a legacy fallback used only when no Session context blocks are configured.
• Emits a deduped [think] warning when getSkills() returns sources and the agent overrides getSystemPrompt().
• Adds a regression test agent that reproduces the getSkills() plus overridden getSystemPrompt() setup and asserts the warning.
• Adds a patch changeset for @cloudflare/think.

---

[changeset-bot]

🦋 Changeset detected

Latest commit: 0b2e6a8

The changes in this PR will be included in the next version bump.

This PR includes changesets to release 2 packages

Name	Type
@cloudflare/think	Patch
@cloudflare/agent-think	Patch

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[devin-ai-integration]

✅ Devin Review: No Issues Found

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