ComponentSet.fromSource() ignores component.isMarkedForDelete() in include filter

### Summary
`ComponentSet.fromSource()` ignores `components` which are `markedForDelete` in `include` filter.

### Steps To Reproduce

- create a `componentSet` with components and mark them for deletion.
- use this `componentSet` as an `include` filter and create a `ComponentSet.fromSource()`

### Expected result
`components` which are `markedForDelete` are not listed in `manifestComponents`

### Actual result
`components` which are `markedForDelete` are listed in `manifestComponents`

### System Information

```json
{
"architecture": "darwin-arm64",
"cliVersion": "@salesforce/cli/2.38.0",
"nodeVersion": "node-v20.11.1",
"osVersion": "Darwin 23.4.0",
"rootPath": "/Users/user/.local/share/sf/client/2.38.0-1a95a96",
"shell": "zsh",
"pluginVersions": [
"@jayree/sfdx-plugin-manifest 3.1.63 (user)",
"@jayree/sfdx-plugin-org 1.2.42 (user)",
"@jayree/sfdx-plugin-prettier 1.3.53 (user)",
"@jayree/sfdx-plugin-source 1.3.50 (user)",
"@oclif/plugin-autocomplete 3.0.13 (core)",
"@oclif/plugin-commands 3.2.2 (core)",
"@oclif/plugin-help 6.0.20 (core)",
"@oclif/plugin-not-found 3.1.2 (core)",
"@oclif/plugin-plugins 5.0.7 (core)",
"@oclif/plugin-search 1.0.21 (core)",
"@oclif/plugin-update 4.2.4 (core)",
"@oclif/plugin-version 2.0.16 (core)",
"@oclif/plugin-warn-if-update-available 3.0.15 (core)",
"@oclif/plugin-which 3.1.7 (core)",
"@salesforce/cli 2.38.0 (core)",
"apex 3.1.4 (core)",
"auth 3.6.0 (core)",
"data 3.3.0 (core)",
"deploy-retrieve 3.6.0 (core)",
"dev 2.3.0 (user)",
"info 3.2.0 (core)",
"limits 3.3.0 (core)",
"marketplace 1.2.0 (core)",
"org 4.1.0 (core)",
"packaging 2.3.0 (core)",
"schema 3.3.0 (core)",
"settings 2.1.2 (core)",
"sobject 1.3.0 (core)",
"source 3.2.3 (core)",
"telemetry 3.2.0 (core)",
"templates 56.1.1 (core)",
"trust 3.6.1 (core)",
"user 3.5.0 (core)",
"oclif-plugin-update-notifier 1.5.68 (user)",
"sfdx-autocmplt 2.9.46 (user)"
]
}
```