Major refactor: organize and split into packages

[feuersteiner]

Refactor plan for Contextrie's new package layout.

Active implementation: #40

Direction

• Keep core focused on source contracts, source implementations, and agent primitives
• Separate indexing and judging into explicit agents
• Let sources own the data they expose for indexing and deep judgment
• Keep CLI, docs, examples, and Python as companion packages around the core library
• Leave composition as the next major pipeline to define

Progress

• Reset the repo layout and seed package scaffolding
• Define core source contracts and exports
• Add indexed source implementations
• Extract indexing into a dedicated agent
• Add source inputs for indexing
• Add judge agent types and exports
• Add deep-judge inputs to sources
• Document core boundaries and source/agent flow
• Scaffold companion packages (cli, docs, examples, python)
• Implement the composer pipeline
• Turn the CLI scaffold into a runnable package
• Add executable examples
• Flesh out the Python package beyond a stub

[feuersteiner]

Superseded by the current multi-package repo layout. Remaining work should live in narrower package-specific issues.