Add distributed similarity search

docs/ctx-07-distributed-workload-protocol.md

@@ -4,9 +4,11 @@
 
 This document is the implementation contract for CTX-07. Its generic protocol,
 registry, strict JSON models, and deterministic reduction ordering are
-implemented in `scimesh/distributed/`. It does not implement a molecular
-planner, reducer, API endpoint, database migration, or final artifact. Until
-CTX-08 and CTX-09 are complete, shard CSVs remain diagnostic partial results.
+implemented in `scimesh/distributed/`. CTX-08 implements the molecular
+similarity-search planner, worker adapter, and pure reducer on top of it. This
+document does not implement a coordinator API endpoint, database migration, or
+durable final artifact. Until CTX-09 is complete, shard CSVs remain diagnostic
+partial results.
 
 The protocol gives local scientific workloads a coordinator-independent way to
 validate a job, plan artifact-backed tasks, and later reduce completed outputs.
@@ -154,7 +156,10 @@ rank,chembl_id,canonical_smiles,similarity
 ```
 
 - `rank` is one-based local rank.
-- `similarity` uses the local CLI's six-decimal formatting.
+- `similarity` uses a round-trip decimal representation of the computed float
+  (for Python, `repr(similarity)`). This preserves exact cross-shard ranking;
+  the reducer writes the user-facing final CSV with the local CLI's six-decimal
+  display formatting.
 - Rows are sorted by `(-similarity, chembl_id, canonical_smiles)` for
   `threshold_direction=greater`, or `(similarity, chembl_id,
   canonical_smiles)` for `less`.
@@ -203,7 +208,7 @@ multiplicity. Reduction is independent of worker completion order and uses
 
 ## Deferred work
 
-CTX-08 implements the similarity-search planner, runner adapter, reducer, and
-comparison against the local CLI. CTX-09 persists the final artifact and job
-state. CTX-10 defines graph-specific triangular block plans; it must not reuse
-the search shard scheme without its pair-coverage invariants.
+CTX-09 materializes the planned shard files as coordinator artifacts, invokes
+the registered reducer once, and persists its final artifact/job state. CTX-10
+defines graph-specific triangular block plans; it must not reuse the search
+shard scheme without its pair-coverage invariants.

docs/worker-daemon-task.md

@@ -122,7 +122,10 @@ Content-Type: application/json
   },
   "metrics": {
     "elapsed_seconds": 12.4,
-    "processed_rows": 10000
+    "scanned_rows": 10000,
+    "valid_molecules": 9876,
+    "invalid_smiles": 124,
+    "matches_emitted": 20
   }
 }
 ```
@@ -189,8 +192,11 @@ class Runner(Protocol):
         """Run one task and return output artifacts plus safe metrics."""
 ```
 
-`SciMeshRunner` should map `workload` and validated parameters to the existing
-SciMesh CLI. For example, a `similarity-search` task invokes:
+`SciMeshRunner` maps an allowlisted workload and validated parameters to the
+local SciMesh reference functions. A planned `similarity-search` task contains
+a resolved `query_smiles` (never `query_id`) and writes one exact local top-k
+partial CSV plus the metrics above. Legacy single-shard tasks may still use the
+CLI compatibility path:
 
 ```text
 scimesh similarity-search <local-input> --query-id ... --output <task-dir>/result.csv