Promote yaml.v3 and go-toml/v2 to direct dependencies

go mod tidy correctly marks these as direct imports now that
semantic_diff.go uses them for YAML and TOML parsing.

Author: SamMorrowDrums

go.mod

@@ -28,7 +28,7 @@ require (
 	github.com/lithammer/fuzzysearch v1.1.8
 	github.com/mailru/easyjson v0.7.7 // indirect
 	github.com/modelcontextprotocol/go-sdk v1.2.0
-	github.com/pelletier/go-toml/v2 v2.2.4 // indirect
+	github.com/pelletier/go-toml/v2 v2.2.4
 	github.com/pmezard/go-difflib v1.0.1-0.20181226105442-5d4384ee4fb2 // indirect
 	github.com/rogpeppe/go-internal v1.13.1 // indirect
 	github.com/sagikazarmark/locafero v0.11.0 // indirect
@@ -50,5 +50,5 @@ require (
 	golang.org/x/text v0.28.0 // indirect
 	gopkg.in/check.v1 v1.0.0-20201130134442-10cb98267c6c // indirect
 	gopkg.in/yaml.v2 v2.4.0 // indirect
-	gopkg.in/yaml.v3 v3.0.1 // indirect
+	gopkg.in/yaml.v3 v3.0.1
 )