Option to embed ALL vault documents, not just recent ~1000

[gunternowy]

Context

I have a large Obsidian vault (~18,500 markdown files, ~1.8 GB) and upgraded from enzyme v0.25.3 to v0.4.6.

With v0.25.3, all documents were chunked and embedded (416,379 chunks). With v0.4.6, only ~1,000-3,000 "recent" documents get embeddings. The rest are indexed (entities, tags, links) but not embedded.

Problem

For my use case (research vault with academic papers, project notes, clippings spanning 10+ years), I need all documents embedded for semantic search via enzyme catalyze. Many important connections are between older papers and current projects. Limiting to recent docs misses these cross-temporal patterns.

Request

Could you add a config option or flag to embed all documents? Something like:

# enzyme-config.yaml
embedding:
  scope: all  # or "recent" (default)

Or a CLI flag:

enzyme init --embed-all

Current workaround

Running v0.25.3 in parallel for full embeddings, but the DB format is incompatible with v0.4.6.

Thanks for the great tool!