refactor: migrate schema output config from flat props to nested schema object

[pyramation]

Summary

Replaces the flat schemaOnly / schemaOnlyOutput / schemaOnlyFilename properties with a nested schema: { enabled, output, filename } object, aligning schema export configuration with the existing nested-object paradigm used by tables, queries, codegen, docs, etc.

Config change:

// Before
{ schemaOnly: true, schemaOnlyOutput: './schemas', schemaOnlyFilename: 'public.graphql' }

// After
{ schema: { enabled: true, output: './schemas', filename: 'public.graphql' } }

CLI change: --schema-only → --schema-enabled, plus new --schema-output and --schema-filename flags.

Files changed across graphql/codegen (types, generate, CLI handler/index, tests) and packages/cli (codegen command, display, README, AGENTS.md).

Review & Testing Checklist for Human

• Behavioral change in generate.ts: The old schemaOnly triggered an early return regardless of other generators being enabled. The new code gates schema export on schemaEnabled && !runReactQuery && !runOrm && !runCli — meaning if a user sets schema: { enabled: true } alongside orm: true, the schema export is silently skipped. Verify this is the desired behavior vs. also exporting SDL when generators run.
• Breaking change with no deprecation: Old schemaOnly/schemaOnlyOutput/schemaOnlyFilename properties are fully removed. Any existing configs or programmatic callers using these will silently stop exporting schemas (no error thrown). Consider whether a runtime warning or migration period is needed.
• CLI breaking change: --schema-only no longer works. Verify no CI scripts, Makefiles, or downstream tooling depend on the old flag name.
• Multi-target filename default: In generateMulti, the fallback filename changed from always being ${name}.graphql to schema?.filename ?? ${name}.graphql. Confirm user-provided filename correctly overrides the per-target default.

Notes

• CHANGELOG.md entries referencing --schema-only were intentionally left untouched (historical records).
• This is a breaking change to both the programmatic API and CLI interface.
• Companion PRs for constructive-skills, constructive-private-skills, and constructive-db are planned to update docs/skills referencing the old syntax.

Link to Devin session: https://app.devin.ai/sessions/a0ac766d75d340d490fd265bfafaac83
Requested by: @pyramation

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