Brooks, the "." you're seeing is a side-effect of IC2 being hosted in IntelliJ IDEA which is fundamentally designed for Java, and Java uses "." as a package component separator. The IDE shows the directory paths that correspond to package paths with ".", but those are really "/"s. You can disable a few Project View options to make it look more like you'd expect, e.g.,
Flatten Packages and
Compact Middle Packages from here:
Generally you'll want your project source root configuration to directly mimic your sfdx-project.json file's package directories, so you'd have a content root corresponding to the project root directory, and within that content root, you'd add each of the package directories as a source root.
Let me know if that doesn't make sense or if it's not working properly after you make these UI config and project config changes.
Regards,
Scott Wells