refactor: add #[non_exhaustive] to public structs and enums (#8)

Prevents semver-breaking changes when adding new fields or variants
to Contig, KnownReference, QueryHeader, ContigMetadata, BuilderError,
and CatalogCommands.

Author: nh13

src/catalog/builder.rs

@@ -15,6 +15,7 @@ use crate::core::types::{Assembly, ReferenceSource};
 use crate::utils::validation::{is_valid_md5, is_valid_sha512t24u};
 
 #[derive(Error, Debug)]
+#[non_exhaustive]
 pub enum BuilderError {
     #[error("IO error: {0}")]
     Io(#[from] std::io::Error),
@@ -101,6 +102,7 @@ impl InputFormat {
 
 /// Metadata for a single contig, collected from multiple sources
 #[derive(Debug, Clone)]
+#[non_exhaustive]
 pub struct ContigMetadata {
     /// Primary name (exact, from first source)
     pub primary_name: String,

src/cli/catalog.rs

@@ -24,6 +24,7 @@ pub struct CatalogArgs {
 }
 
 #[derive(Subcommand)]
+#[non_exhaustive]
 pub enum CatalogCommands {
     /// List all references in the catalog
     List {

src/core/contig.rs

@@ -41,6 +41,7 @@ impl SequenceRole {
 
 /// A single contig/sequence in a reference genome
 #[derive(Debug, Clone, PartialEq, Eq, Serialize, Deserialize)]
+#[non_exhaustive]
 pub struct Contig {
     /// Sequence name (SN tag in SAM)
     pub name: String,

src/core/header.rs

@@ -16,6 +16,7 @@ fn count_to_f64(count: usize) -> f64 {
 
 /// A query header extracted from a BAM/SAM/CRAM file
 #[derive(Debug, Clone, Serialize, Deserialize)]
+#[non_exhaustive]
 pub struct QueryHeader {
     /// Source file path (if known)
     #[serde(default, skip_serializing_if = "Option::is_none")]

src/core/reference.rs

@@ -7,6 +7,7 @@ use crate::utils::validation::compute_signature as compute_sig;
 
 /// A known reference genome in the catalog
 #[derive(Debug, Clone, Serialize, Deserialize)]
+#[non_exhaustive]
 pub struct KnownReference {
     /// Unique identifier
     pub id: ReferenceId,