BM25 search returns fewer results when multiple -c collection flags are used

[jennaWILDE]

Bug Description

When using qmd search with multiple -c (collection) flags, significantly fewer results are returned compared to searching without any collection filter.

Steps to Reproduce

Given an index with multiple collections (e.g. notes, docs, sessions):

# Without collection filter — returns 5 results, scores 0.94-0.96
qmd search "Plugin Development Bootstrap" --json -n 8

# With all collections explicitly listed — returns only 1 result
qmd search "Plugin Development Bootstrap" --json -n 8 -c notes -c docs -c sessions

Expected Behavior

Specifying all collections via -c flags should return the same results as not specifying any collection filter (which implicitly searches all collections).

Actual Behavior

Multi-collection search returns significantly fewer results. In the example above:

• No -c flags: 5 results (scores 0.94–0.96), including matches from notes and docs collections
• All -c flags: Only 1 result (from sessions)

Results from notes and docs collections are lost when explicitly filtering.

Environment

• qmd 1.0.0
• Node.js v25.5.0
• macOS (Apple Silicon)
• Index: ~700 files across 4 collections, ~1300 embeddings

Workaround

Omitting the -c flags and searching across all collections works correctly.