Restore citation metadata for XML prompts

[bmdavis419]

Greptile Summary

This PR refactors the agent instruction format from plain text lines to structured XML, restoring citation metadata for XML-aware prompts. It also introduces a richer BASE_PROMPT constant in loop.ts with explicit persona, tool-calling, and output-contract sections.

• service.ts: createCollectionInstructionBlock now outputs XML (<resource>, <repo_url>, <github_blob_prefix>, <focus_paths>, etc.) using new escapeXml, xmlLine, and xmlPathBlock helpers; a new createCollectionInstructions wrapper wraps all resources in <available_resources>.
• loop.ts: Old inline prompt string replaced by a BASE_PROMPT constant; buildSystemPrompt now simply concatenates BASE_PROMPT and agentInstructions.
• service.test.ts: Test helpers made more flexible; two new tests verify git and npm XML citation metadata fields end-to-end.
• Convex generated files (api.d.ts, server.d.ts, api.js, dataModel.d.ts, server.js): Formatting-only changes (double → single quotes, 2-space → tab indent).
• Version bumped from 2.0.3 → 2.0.4 in CLI, server packages, and bun.lock; @typescript/native-preview dev dependency updated.

Confidence Score: 4/5

• Safe to merge; the format change is well-tested and intentional, with two minor style nits around the npm citation rule.
• The core logic change (plain-text → XML instructions) is covered by new unit tests and doesn't touch any data model or API contracts. The two flagged issues are style-level concerns in LLM instruction text, not functional regressions. Generated Convex files are formatting-only.
• apps/server/src/collections/service.ts — review the npm citation_rule string for the XML-escaped <file> placeholder and the version-missing fallback text.

Important Files Changed

Filename	Overview
apps/server/src/collections/service.ts	Core change: refactors agentInstructions output from plain text to XML format using new escapeXml helper and structured xmlLine/xmlPathBlock utilities. Two minor issues: the <file> placeholder in the npm citation rule gets XML-escaped to &lt;file&gt;, and the fallback text when npm version metadata is missing produces a confusing LLM instruction.
apps/server/src/collections/service.test.ts	Test helpers refactored to be more flexible; two new tests added for git and npm citation metadata in agent instructions. Coverage looks thorough for the new XML format.
apps/server/src/agent/loop.ts	Adds a new BASE_PROMPT constant with detailed XML-structured system prompt instructions (persona, tool-calling rules, output contract) and simplifies buildSystemPrompt to concatenate BASE_PROMPT with agentInstructions.

_{Last reviewed commit: dd7275a}

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Project	Deployment	Actions	Updated (UTC)
better-context	Ready	Preview, Comment	Mar 5, 2026 8:34pm

[bmdavis419]

• Restore citation metadata for XML prompts #208 👈 (View in Graphite)
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[greptile-apps]

Typo: "through" should be "thorough"

"be through with your response" is grammatically incorrect — it should be "be thorough with your response" (meaning detailed/complete).

Suggested change

	- Default follow-through: don't ask permission to do the research, just do it and answer the question. ask for clarifications + suggest good follow up if needed
	- Length: be thorough with your response, don't let it get too long though

Prompt To Fix With AI

This is a comment left during a code review.
Path: apps/server/src/agent/loop.ts
Line: 69

Comment:
Typo: "through" should be "thorough"

"be through with your response" is grammatically incorrect — it should be "be thorough with your response" (meaning detailed/complete).

```suggestion
- Length: be thorough with your response, don't let it get too long though
```

How can I resolve this? If you propose a fix, please make it concise.

_{Note: If this suggestion doesn't match your team's coding style, reply to this and let me know. I'll remember it for next time!}

[greptile-apps]

Typo: "through" should be "thorough"

Same issue as above — "Return a through answer" should be "Return a thorough answer".

Suggested change

	- Return a through answer to the user's question with real code examples
	- Return a thorough answer to the user's question with real code examples

Prompt To Fix With AI

This is a comment left during a code review.
Path: apps/server/src/agent/loop.ts
Line: 99

Comment:
Typo: "through" should be "thorough"

Same issue as above — "Return a through answer" should be "Return a thorough answer".

```suggestion
- Return a thorough answer to the user's question with real code examples
```

How can I resolve this? If you propose a fix, please make it concise.