to_obsidian wrote one note per node straight into the target directory and
unconditionally replaced .obsidian/graph.json. Pointing --obsidian-dir at a real
vault could therefore clobber a user note whose name matched a graph node
(Database.md) and destroy the user's graph-view settings — silently, no backup,
irreversible.
graphify now records the files it owns in .graphify_obsidian_manifest.json and
refuses to overwrite any pre-existing file it didn't create: such a file is skipped
and reported in a single aggregated warning. A re-run still updates graphify's own
notes (they're in the manifest), and .obsidian/graph.json is only written when it
doesn't already exist or graphify owns it. The default graphify-out/obsidian output
and the flat note layout are unchanged.
Added regression tests: existing-vault preserves user note + .obsidian settings,
empty dir still gets the full vault, and a re-run updates own notes but not a
user-added file. The CHANGELOG also records the @oleksii-tumanov Java fixes
(#1512/#1510) and the @nuthalapativarun Windows GBK fix (#1505) committed just prior.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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