Add dynamic agent-mode query pipeline #55
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* Introduced ContextRegistry, AgentOrchestrator, and AgentToolkit to run a budgeted investigation and synthesis loop over existing artifacts. * Wired agent mode into config and CLI with reasoning and tool limits, plus a new model and tools for search, navigational reading, grep, and section summaries. * Current agent loop is a first cut with simple prompts, no registry scoring or eviction policy, and some hardcoded paths and basic error handling.
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Note: Much of the code is AI generated. I am sharing this PR as a POC, and working on the details.