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The gettext build emitted 23251 warnings. Three causes carried 22424 of them, and each is answered with the mechanism sphinx supplies. conf.py read .yml and .yaml through the reStructuredText parser, where yaml indentation is a block quote: 16107 warnings, and the pages had no title either. A parser renders them as the literal block they are, and marks them orphan because a yaml file is reference material rather than a chapter, which drops another 3062 toctree warnings. myst builds a document reference only when the link target is_file(), so every link to a directory fell through as unresolvable. A post-transform ahead of myst's resolver points such a link at the directory's README, but only where that README exists, which leaves the genuinely dangling ones reported. Together with myst_heading_anchors, which was never configured, that clears 2921 missing cross-references and 320 python references. Measured per step over four full builds: 23251 -> 7130 -> 4068 -> 827. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>