fix(deps): declare pyyaml as a base dependency

The 0.9.95 YAML structural extractor (#4706) imports PyYAML, but it was
only a transitive dependency, so a fresh `pip install graphifyy` produced
zero nodes from .yaml/.yml files (the extractor degrades gracefully but
silently). manifest_ingest and markdown also use it via guarded imports.
Declare it like tree-sitter-json so the feature works out of the box.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

pyproject.toml

@@ -15,6 +15,8 @@ dependencies = [
     "networkx>=3.4",
     "numpy>=1.21",
     "rapidfuzz>=3.0",
+    # Structural YAML extraction (#2214) plus manifest/markdown config parsing.
+    "pyyaml>=6.0",
     "tomli>=2.0.1; python_version < '3.11'",
     # Runtime floor is 0.25, not 0.23: 0.23/0.24 cap out at ABI 14
     # (LANGUAGE_VERSION=14) while the grammars pinned below ship ABI 15