Uninstall a module with a FileCopy resource shouldn't delete the entire directory

## Describe the bug
If a module copy files into a shared directory and you uninstall that module, the shared directory would be deleted. As an example, HealthConnect.FHIRMeta and HealthConnect.FHIRMeta.R5 both copy files into /dev/fhir/fhir-metadata/. I have a solution module that only needs HealthConnect.FHIRMeta. When I uninstall my solution module, the entire /dev/fhir/fhir-metadata/ directory is deleted.

## To Reproduce
Steps to reproduce the behavior:
1. Run IPM command 'install HealthConnect.FHIRMeta'
2. Verify the following 3 packages are copied into instance directory /dev/fhir/fhir-metadata/packages: hl7.fhir.r3.core, hl7.fhir.r4.core, hl7.fhir.us.core
4. Run IPM command 'install HealthConnect.FHIRMeta.R5'
5. Verify the following 1 package is copied into instance directory /dev/fhir/fhir-metadata/packages: hl7.fhir.r5.core
6. Run IPM command 'uninstall HealthConnect.FHIRMeta'
7. Verify the issue: the entire /dev/fhir/fhir-metadata/ directory is deleted.

## Expected Behavior
A FileCopy resource has Overlay=1 should keep track of its files and only delete those on uninstall instead of the entire directory. In this example, /dev/fhir/fhir-metadata/ should exist with 1 package: hl7.fhir.r5.core. Also, if an overlay=1 FileCopy sees an identically named existing file, show a warning, but don't fail.

## System information (please complete the following information):
- IPM version: 0.10.4
- IRIS version: IRIS for UNIX (Apple macOS for Apple Silicon) 2025.1.2 (Build 349U)
- OS: Apple macOS for Apple Silicon
- Docker or local: local