Cortex stores repository content, metadata, Git summaries, episodic events, environment profiles, and neural associations locally. Protect CORTEX_HOME as repository-sensitive data.

Exclude secret-bearing files before bootstrap. Do not record credentials, tokens, personal data, or raw confidential logs as episodic events.

Environment profiles, Discovery Cards, relationship resolution, and neural association weights may be incomplete or wrong. They are routing evidence, not authority.

Plasticity can only update bounded internal association weights for existing compiled relationships. It cannot change source files, create arbitrary graph topology, or operate in read_only mode.

Cortex never authorizes durable repository mutation. Current source, current tests, compiler/runtime evidence, host repository rules, and explicit human authorization control changes.

A bootstrap certificate verifies the implemented inventory, integration, environment, neural compilation, and retrieval checks at a manifest. It is not a security audit or correctness proof.