feat: add system_prompt and allowed_tools to kernel contract

[broomva]

Summary

• Adds system_prompt: Option<String> to ModelCompletionRequest for liquid prompt injection
• Adds allowed_tools: Option<Vec<String>> to ModelCompletionRequest for skill-based tool filtering
• Extends TickInput with both fields, threaded through to provider calls

Part of the Arcan Skill System Evolution (6-phase implementation). This is the protocol-level foundation that enables skills to inject context and restrict tools.

Test plan

• All 102 aiOS workspace tests pass
• Backward compatible (new fields are Option with serde(default))
• Arcan adapter consumes both fields correctly

🤖 Generated with Claude Code

Summary by CodeRabbit

• New Features
  • Added system prompt configuration for language model requests
  • Added tool filtering to restrict available tools
  • Added mode change event tracking with transition reasons
  • Enhanced observability with distributed tracing integration and trace correlation
  • Added operational metrics for mode transitions and tool execution tracking

[coderabbitai]

Caution

Review failed

Pull request was closed or merged during review

📝 Walkthrough

Walkthrough

A new vigil workspace dependency is introduced for observability, and the kernel/runtime gain support for system prompts and allowed tools filtering in LLM requests. The runtime adds mode change tracking with event emission and enhanced observability through OpenTelemetry tracing and metrics recording.

Changes

Cohort / File(s)	Summary
Dependency Management Cargo.toml, crates/aios-runtime/Cargo.toml	Added workspace dependency for vigil, and introduced tracing-opentelemetry (0.30) and opentelemetry (0.29) for enhanced observability.
Protocol Updates crates/aios-protocol/src/ports.rs	Extended ModelCompletionRequest with optional system_prompt and allowed_tools fields for LLM request customization.
Kernel Integration crates/aios-kernel/src/lib.rs	Updated TickInput construction in tick_on_branch to explicitly populate system_prompt and allowed_tools fields as None.
Runtime Core crates/aios-runtime/src/lib.rs	Enhanced TickInput struct with system_prompt and allowed_tools fields; threaded these into LLM requests. Added per-tick counters, mode change tracking with event emission, metrics recording for GenAI budget and mode transitions, OpenTelemetry span instrumentation, and trace context embedding in event records.

Sequence Diagram

sequenceDiagram
    participant Kernel as AiosKernel
    participant Runtime as AiosRuntime
    participant LLM as LLM Model
    
    Kernel->>Runtime: tick_on_branch with TickInput<br/>(system_prompt, allowed_tools)
    Runtime->>Runtime: Perceive: Record GenAI<br/>budget metrics
    Runtime->>Runtime: Reflect: Create ModelCompletionRequest<br/>populate system_prompt, allowed_tools
    Runtime->>LLM: Send request with custom<br/>system prompt & filtered tools
    LLM-->>Runtime: Model completion response
    Runtime->>Runtime: Record mode transition<br/>& emit EventKind::ModeChanged
    Runtime->>Runtime: Write trace context to<br/>event records (OTel integration)
    Runtime-->>Kernel: Return tick result with<br/>events & observability data

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Estimated code review effort

🎯 4 (Complex) | ⏱️ ~60 minutes

Poem

🐰 Hop, hop! A new vigil keeps watch,
System prompts whisper, tools carefully notched,
OpenTelemetry traces the way,
Mode changes gleam in telemetry's display,
Events now carry their story so bright,
Every tick traced by observability's light! ✨

🚥 Pre-merge checks | ✅ 2 | ❌ 1

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Docstring Coverage	⚠️ Warning	Docstring coverage is 66.67% which is insufficient. The required threshold is 80.00%.	Write docstrings for the functions missing them to satisfy the coverage threshold.

✅ Passed checks (2 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The PR title accurately and concisely summarizes the primary change: adding system_prompt and allowed_tools fields to the kernel contract (ModelCompletionRequest and TickInput).

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✨ Finishing Touches

📝 Generate docstrings

• Create stacked PR
• Commit on current branch

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch feat/skill-system-liquid-prompt

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