Include tool nodes in doc DAG so their compile layers are stacked
Tool packages like ocaml-compiler have documentable libraries
(stdlib) but aren't in the regular build DAG — they're only in
the tool DAG. Without indexing them in build_by_hash and creating
doc nodes for them, find_dep_compile_layers can't find their
compile layers, causing unresolved cross-references (e.g.
Stdlib.Format.formatter in base's docs).
Fix: add tool nodes to build_by_hash, derive their compilers,
and include them in the doc node creation loop so they get
compile/doc-all nodes and appear in build_to_doc_hash.
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>