Preserve permissions by default and fix warnings (apple#496)

Permissions should be preserved when copying by default. This PR also
fixes other warnings while building and testing.

Author: dkovba

Sources/NativeBuilder/ContainerBuildIR/Graph/GraphBuilder.swift

@@ -219,7 +219,7 @@ public final class GraphBuilder {
             destination: destination,
             fileMetadata: FileMetadata(
                 ownership: chown,
-                permissions: chmod
+                permissions: chmod ?? .preserve
             )
         )
 

Tests/NativeBuilderTests/ContainerBuildIRTests/DigestAndPlatformTests.swift

@@ -263,7 +263,7 @@ struct DigestAndPlatformTests {
 
     @Test func digestErrorMessages() throws {
         do {
-            try Digest(algorithm: .sha256, bytes: Data(count: 16))
+            _ = try Digest(algorithm: .sha256, bytes: Data(count: 16))
             Issue.record("Should have thrown an error")
         } catch let error as DigestError {
             switch error {
@@ -278,7 +278,7 @@ struct DigestAndPlatformTests {
         }
 
         do {
-            try Digest(parsing: "invalid:format")
+            _ = try Digest(parsing: "invalid:format")
             Issue.record("Should have thrown an error")
         } catch let error as DigestError {
             switch error {
@@ -291,7 +291,7 @@ struct DigestAndPlatformTests {
         }
 
         do {
-            try Digest(parsing: "sha256:invalid-hex")
+            _ = try Digest(parsing: "sha256:invalid-hex")
             Issue.record("Should have thrown an error")
         } catch let error as DigestError {
             switch error {

Tests/NativeBuilderTests/ContainerBuildIRTests/SerializationTests.swift

@@ -267,8 +267,10 @@ struct SerializationTests {
 
         // Check for COPY operation with metadata
         let copyOps = stage.nodes.compactMap { $0.operation as? FilesystemOperation }
-        let copyWithMetadata = copyOps.first { $0.fileMetadata != nil }
-        #expect(copyWithMetadata != nil, "COPY operation with metadata should be preserved")
+        let copyWithMetadata = copyOps.first {
+            $0.fileMetadata.permissions != nil
+        }
+        #expect(copyWithMetadata != nil, "COPY operation should preserve file permissions by default")
 
         // Check for metadata operations
         let metaOps = stage.nodes.compactMap { $0.operation as? MetadataOperation }