docs: clarify query pipeline, Findere trick, and input formats

Fix a stray prefix in the README heading and update documentation to reflect the query pipeline's operation on `s-mers` (`s = k - z + 1`) with post-partition z-window filtering. Clarify the Findere trick, including k-mer size reduction, consecutive match requirements, and false positive rate calculations. Additionally, expand input format documentation to cover supported file extensions, gzip compression, recursive directory handling, and `query` command specifications.

docmd/implementation/evidence_elimination.md

@@ -35,15 +35,18 @@ stored at `s` belongs to the legitimate k-mer at that slot. The FP event is:
 P(FP per k-mer) = 1 / 2^b
 ```
 
-The Findere trick raises the effective window to z consecutive k-mers. A query
-succeeds only when all z fingerprint checks pass, reducing the per-window FP rate:
+The Findere trick reduces the indexed k-mer size. When the user specifies k_user
+and z, the index physically stores k-mers of size `s = k_user − z + 1`. At query
+time, the same s-mer size is used. After collecting per-position s-mer results
+over the full query sequence, a sliding window of size z aggregates z consecutive
+s-mer hits into one confirmed k_user-mer hit, reducing the per-window FP rate:
 
 ```
-P(FP per z-window) = 1 / 2^(b·z)
+P(FP per k_user-mer) = 1 / 2^(b·z)
 ```
 
-The effective indexed k-mer length is `k − z + 1`: a query for a (k+z−1)-mer
-decomposes into z overlapping k-mers, all of which must match.
+`IndexConfig::kmer_size` stores `s = k_user − z + 1`, not k_user. Both indexing
+and querying use this stored size via `set_k(idx.kmer_size())`.
 
 Parameters b and z are stored in `layer_meta.json` (`EvidenceKind::Approx { b, z }`).
 
@@ -167,12 +170,12 @@ any index. It accepts the same `--evidence-bits`, `-z`, and `--fp` flags and
 additionally accepts `-k` to display the effective indexed k-mer length:
 
 ```
-k (query):             31
-k (indexed):           31
-z:                     1
+k (user):              31
+k (indexed, s=k-z+1):  27
+z:                     5
 evidence bits (b):     8
-FP per k-mer:          3.906e-3  (1/2^8)
-FP per z-window:       3.906e-3  (1/2^8)
+FP per s-mer:          3.906e-3  (1/2^8)
+FP per k-mer window:   9.537e-7  (1/2^(8·5))
 ```
 
 Useful for choosing parameters before committing to an index build.