filesystem mcp: dot directories should be ignored

Describe the bug
Dot directories (eg .git, .terraform, etc) are included in the filesystem MCP search tools.

These directories, particularly .git can get enormous and thus massively inflate the token usage for the agent.

What's more, these directories generally don't add much value (they're "hidden" for a reason) for project analysis. And in the worst case scenarios, might even contain sensitive information.

Personally, I'd go further and say allowing filesystem to work against any dot-prefixed filesystem objects is a security risk, however, for the sake of wanting to keep this discussion focused on reducing token count rather than whether users should or should not be aware of what data they're sharing with the agent, this GH Issue is focused on dot-prefixed directories like .git.

To Reproduce
Run the MCP with the authorised path being the root of any project that is also a git repository.

Expected behavior
Dot-prefixed directories should be ignored by default. An environmental variable and/or command line flag can be used to optionally re-enable this behaviour.

Logs

Additional context
While the intended behaviour is to selectively include the files and/or directories you wish to authorise for use with this MCP, the benefit of using an MCP like this is for speed and convenience. Thus a typical use case might well be someone selecting the entire project directory. On the surface, this is a pragmatic approach -- so long as dot-prefixed directories (and arguably files too) are ignored by default.

Start at the filesystem MCP search tools and reproduce the issue with an authorised project root containing .git or .terraform. Trace how directory entries are selected, then verify that dot-prefixed directories are excluded by default and that the chosen environment-variable or command-line opt-in restores them.