feat(config): apply top-level runtime settings

[yan-ad]

Summary

• Load configured instruction files into system prompts.
• Apply global tool permissions, watcher settings, and enabled/disabled provider filters.
• Parse compaction and formatter settings, and document their current compatibility status.

Validation

• cargo fmt --all
• cargo test config::configuration::tests::parses_and_applies_top_level_runtime_configuration

[Blankeos]

Nice work on this. The parsing and print-mode wiring looked solid.

Merge confidence: 4/5

My agent found a bug.. I reproduced the gap with:

1. Add a tools and instructions config

// ~/.config/crabcode/crabcode.jsonc
{
  "tools": { "bash": false },
  "instructions": ["~/dotfiles/CUSTOM.md"]
}

2. CUSTOM.md saying “Always begin every response with CUSTOM-INSTRUCTION.”
3. crabcode -p "hi" honored it;
4. a normal interactive TUI session did not (bash still available, no
   custom instruction).

The new commit fixes that.

[Blankeos]

Merge confidence: 4.8/5

New change: Unify config → runtime assembly in ConfigRuntime so both entrypoints share one place for permissions, discovery, and instructions — with unit tests covering tool disable, instructions, provider filters, and print-mode interactive-tool denies.

LGTM from my side