[mauripunzueta]

Closes #2008.

What

A metadata-only $reindex mode that fills in missing_params on MongoDB resources written before #1984, without rebuilding the value index.

{"resourceType": "Parameters", "parameter": [
  {"name": "metadataOnly", "valueBoolean": true},
  {"name": "skipExistingMetadata", "valueBoolean": true}
]}

• metadataOnly: same walk, same extraction (search_index_documents_checked) and same version guard (resource_version_filter, upsert: false) as a rebuild. Only the resources.missing_params update runs; nothing is deleted from or inserted into search_index / search_index_contained.
• skipExistingMetadata: adds missing_params: {$exists: false} to each update's filter, so resources that already carry the field are left alone.
• $reindex-status adds metadataOnly: true and metadataUpdated, the number of resources the updates matched. entriesCreated stays 0. Per-resource failures are reported as they are today.
• Validation: 400 when combined with clearExisting, clearOnly or a bulk index rebuild, and 400 for skipExistingMetadata without metadataOnly. It does combine with POST /{type}/$reindex, with idStart/idEnd, and with named resources.
• 501 on every backend except MongoDB, including MongoDB with search offloaded (mongodb-elasticsearch never reads missing_params). This is checked before a job id is issued.

How

• ReindexTarget gains supports_search_metadata() (default false) and write_search_metadata_page() (default: refuse). In metadata mode the driver writes only through writers that support it.
• MongoDB: a new write_metadata_page in reindex_pipeline.rs. It reuses extract_one (on the rayon pool for large pages), update_missing_metadata (now with a counted variant) and page_outcomes.
• Docs: in docs/mongodb/search-indexes.md, upgrade step 3 now uses metadataOnly, and there is a new "Metadata-only reindex" section. The definition-maintenance procedure still says full rebuild, because its value-index rows were extracted under the old definitions too. The issue suggested this mode for that case as well, but that would leave stale value rows behind.

Acceptance criteria

• After a metadata-only run on a pre-feat(mongodb): index missing search parameters on resources #1984 dataset, every live resource has missing_params, and search_index is untouched. mongodb_metadata_only_reindex_backfills_without_touching_the_index unsets the field across a tenant, runs the mode, and asserts that the stored arrays equal what the original writes stored. It also asserts that every search_index + search_index_contained row is byte-for-byte identical, including _id, so a rewrite would show, and that a second tenant is untouched.
• :missing=true results are identical before and after. The same test checks birthdate:missing=true and =false both ways.
• Documented in docs/mongodb/search-indexes.md.

Also covered: skipExistingMetadata keeps a sentinel array and respects type scope, offloaded MongoDB returns Unsupported, plus REST parse and validation unit tests.

Verified locally

• cargo test -p helios-persistence --features mongodb --test mongodb_tests reindex: 81 passed, including the 3 new tests, against a real MongoDB testcontainer.
• cargo test -p helios-persistence --features mongodb --lib reindex: 167 passed.
• cargo test -p helios-rest --lib reindex: 20 passed.
• clippy: no new warnings on the changed lines. The local toolchain flags collapsible_if on existing code.

Not done / follow-ups

• skipExistingMetadata skips only the write. Every resource in scope is still read and extracted, because the reindex source has no "field absent" filter. Pushing missing_params: {$exists: false} into the Mongo walk (id phase and catch-up rounds) would make a mostly-backfilled tenant cheap to re-run. I left it out to keep the walk untouched.
• Not run at scale. No measurement yet of the metadata-only throughput against a full rebuild on the Synthea corpus.

[codecov]

Codecov Report

❌ Patch coverage is 84.18972% with 40 lines in your changes missing coverage. Please review.

Files with missing lines	Patch %	Lines
crates/persistence/src/search/reindex.rs	77.96%	26 Missing ⚠️
crates/persistence/src/backends/mongodb/storage.rs	38.46%	8 Missing ⚠️
...rsistence/src/backends/mongodb/reindex_pipeline.rs	91.17%	6 Missing ⚠️

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