Fix bug 1008: The vlog_parser checks if any packages are used by a source file and in case adds them to file's dependencies.

Fix bug 1007: the ParserFactory checks instance of a SourceFile instead of checking file's extension.

Files can depend on other files that fall into two categories: included and compiled. The former don't need marker files(.name) and the dependency is directly on the included file. The latter need a marker file and the dependency is built on it. To check whether a file is compiled or included, we see if a file is in the manifests. If an included file will show up in one of the manifest, this rule will be broken and a buggy makefile will be produced.

This reverts commit dc267836.