Adding project_excludes config wipes the default directories

[migeed-z]

Describe the Bug

We default to excluding things like venv or .github.

Defining a project_excludes in a config by default wipes those options. However, a user may want to exclude some directories but does not want to necessarily include venv etc,

Sandbox Link

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(Only applicable for extension issues) IDE Information

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[stroxler]

Note that this issue implicitly affects pyrefly init, although fixing it at the config level might implicitly fix pyrefly init