Improve onboarding, secure and extend automation hooks

[dacorvo]

This pull request updates the documentation to clarify terminology, improve instructions, and simplify the setup process for funes. The main focus is to consistently use "store" instead of "index", clarify the agent-agnostic and local-first nature of funes, and streamline the automation scripts section by replacing lengthy inline scripts with references to reusable scripts. The changes also improve explanations of sharing, caching, and security.
Finally, this protects all write operations to a store behind a lock, and adds a funes guide CLI comment to ease onboarding.

[Copilot]

Pull request overview

This PR updates funes’ onboarding and automation guidance while also extending the CLI/runtime to better support “local store” terminology and safer local-store mutation.

Changes:

• Added an in-binary local-store writer lock and integration coverage to fail loudly on contention.
• Introduced a new funes guide command and refreshed onboarding text to be more agent-agnostic.
• Streamlined automation setup by referencing reusable hook scripts and updating docs/strings toward “store” terminology.

Reviewed changes

Copilot reviewed 15 out of 15 changed files in this pull request and generated 10 comments.

Show a summary per file

File	Description
tests/store_lock.rs	New integration test validating store-lock contention behavior.
src/lock.rs	New StoreLock implementation for serializing local-store writers.
src/index.rs	Acquires the store lock for the duration of indexing to avoid concurrent mutation.
src/scrub.rs	Acquires the store lock for scrubbing (row rewrite) to ensure exclusive writer access.
src/recall.rs	Normalizes --harness values so CLI spellings filter correctly (e.g., claude → claude_code).
src/mcp.rs	Updates MCP schema description for harness values to match CLI spellings.
src/main.rs	Adds guide subcommand wiring and updates CLI help strings toward “store”.
src/hello.rs	Updates built-in passages and adds a human-readable guide() output.
src/lib.rs	Exposes the new lock module.
scripts/automation/funes-index.sh	New reusable per-turn indexing hook script.
scripts/automation/funes-push.sh	New reusable per-session-boundary push hook script.
README.md	Onboarding updated to prefer funes guide and “store” terminology.
docs/automation.md	Reworked automation doc to install/use reusable scripts and document multi-agent hooks.
docs/storage.md	Minor wording update around local re-index cleanup behavior.
docs/RATIONALE.md	Terminology updates from “index” to “store” in rationale.

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