Fix stale comments referencing deleted config type names

Update references to WorkflowRunConfig, ServerConfig, apply_defaults,
and deny_unknown_fields in comments and docs to reflect the FabroConfig
unification.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

docs/api-reference/fabro-api.yaml

@@ -3990,7 +3990,7 @@ components:
     # ── Configuration Schemas ────────────────────────────────────────────
 
     RunConfiguration:
-      description: Structured run configuration mirroring WorkflowRunConfig.
+      description: Structured run configuration mirroring FabroConfig.
       type: object
       required:
         - version
@@ -4262,7 +4262,7 @@ components:
           description: Whether hook runs in sandbox.
 
     ServerConfiguration:
-      description: Structured server configuration mirroring ServerConfig.
+      description: Structured server configuration mirroring FabroConfig.
       type: object
       properties:
         data_dir:

docs/execution/run-configuration.mdx

@@ -485,7 +485,7 @@ Fabro validates the run config when it loads:
 
 - **Version check** — Only `version = 1` is accepted. Other versions are rejected immediately.
 - **Required fields** — `version` and `graph` are required. `goal` is optional (can be provided via `--goal` or Graphviz graph attribute).
-- **Unknown fields** — Extra fields not listed above are rejected (`deny_unknown_fields`).
+- **Unknown fields** — Extra fields not listed above are silently ignored.
 - **Variable check** — Any `$variable` in the Graphviz file without a matching `[vars]` entry produces an error.
 
 Use `--preflight` to validate a run config without executing it:

lib/crates/fabro-cli/src/commands/run.rs

@@ -406,7 +406,7 @@ pub(crate) fn resolve_ssh_clone_params(
 
 /// Resolve the fallback chain from config.
 ///
-/// `apply_defaults` must be called on `run_cfg` before this — it merges
+/// `merge_overlay` must be called before this — it merges
 /// `run_defaults.llm.fallbacks` into `run_cfg.llm.fallbacks` already.
 pub(crate) fn resolve_fallback_chain(
     provider: Provider,
@@ -792,7 +792,7 @@ pub async fn run_command(
     // Serialize the merged run config so the run dir is self-contained.
     // Skip when the workflow path is already the cached run.toml (i.e. _run_engine
     // restart) — create_run already wrote the correct snapshot and re-writing here
-    // would persist a double-applied config (apply_defaults ran again on load).
+    // would persist a double-merged config (merge_overlay ran again on load).
     let is_cached_snapshot = workflow_path
         .file_name()
         .is_some_and(|f| f == RUN_CONFIG_FILE);