fix(core): simplify tool schemas

[rekram1-node]

Summary

• use exact optional keys for built-in tool and filesystem schemas
• flatten compatible Effect allOf constraints and inline local schema references
• add a script for inspecting the exact model-facing schema of built-in tools

Testing

• bun test test/tool-schema.test.ts test/tool-read-filesystem.test.ts
• bun typecheck
• git diff --check