r/sedonadb: Clear file-related check warnings

We have a few warnings in R CMD check that would be nice to clear up:

```
Found the following hidden files and directories:
src/c/.clang-format
src/c/sedona-s2geography/s2geography/.clang-format
src/c/sedona-s2geography/s2geography/.editorconfig
src/c/sedona-s2geography/s2geography/.git
src/c/sedona-s2geography/s2geography/.pre-commit-config.yaml
src/c/sedona-s2geography/s2geometry/.git
src/c/sedona-s2geography/s2geometry/.travis.yml
src/c/sedona-s2geography/s2geography/.github
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... NOTE
Found the following non-portable file paths:
sedonadb/src/rust/sedona-geo-generic-alg/src/algorithm/line_measures/metric_spaces/euclidean/distance.rs
sedonadb/src/rust/sedona-geo-generic-alg/src/algorithm/line_measures/metric_spaces/euclidean/utils.rs

Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.

```

For the hidden files I think we just remove these when we run `bootstrap.R` to create the source tarball.

For the non-portable file paths it's probably just easiest to shorten the name `sedona-geo-generic-alg` (we only need a few characters back).

While we're here we should see if we can ensure that the r-extended CI job fails on notes or warnings we don't expect.

Start with bootstrap.R and the r-extended CI job, then inspect the listed src/c hidden files and the long paths under sedonadb/src/rust/sedona-geo-generic-alg. Done means the source tarball no longer reports unintended hidden files or non-portable paths, and the CI job fails on unexpected R CMD check notes or warnings.

Written by the indexing model from the issue text.