Thanks for the clarification. I'm not exactly sure why those particular files are showing up as new files. Did you recently upgrade the rmarkdown package? Every time you run render_site(), the site_libs/ directory is deleted and re-created. The reproducible example below shows that those font files are included by default, so I would have expected them to already be committed in your repository:
directory <- tempfile()
dir.create(directory)
yaml <- file.path(directory, "_site.yml")
writeLines("output_dir: \"docs\"", con = yaml)
index <- file.path(directory, "index.Rmd")
file.create(index)
#> [1] TRUE
rmarkdown::render_site(directory, quiet = TRUE)
list.files(file.path(directory, "docs", "site_libs", "bootstrap-3.3.5", "css", "fonts"))
#> [1] "Lato.ttf" "LatoBold.ttf"
#> [3] "LatoItalic.ttf" "NewsCycle.ttf"
#> [5] "NewsCycleBold.ttf" "OpenSans.ttf"
#> [7] "OpenSansBold.ttf" "OpenSansBoldItalic.ttf"
#> [9] "OpenSansItalic.ttf" "OpenSansLight.ttf"
#> [11] "OpenSansLightItalic.ttf" "Raleway.ttf"
#> [13] "RalewayBold.ttf" "Roboto.ttf"
#> [15] "RobotoBold.ttf" "RobotoLight.ttf"
#> [17] "RobotoMedium.ttf" "SourceSansPro.ttf"
#> [19] "SourceSansProBold.ttf" "SourceSansProItalic.ttf"
#> [21] "SourceSansProLight.ttf" "Ubuntu.ttf"
Created on 2020-05-23 by the reprex package (v0.3.0)
Session info
devtools::session_info()
#> - Session info ---------------------------------------------------------------
#> setting value
#> version R version 4.0.0 (2020-04-24)
#> os Windows 10 x64
#> system x86_64, mingw32
#> ui RTerm
#> language (EN)
#> collate English_United States.1252
#> ctype English_United States.1252
#> tz America/New_York
#> date 2020-05-23
#>
#> - Packages -------------------------------------------------------------------
#> package * version date lib source
#> assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.0.0)
#> backports 1.1.6 2020-04-05 [1] CRAN (R 4.0.0)
#> callr 3.4.3 2020-03-28 [1] CRAN (R 4.0.0)
#> cli 2.0.2 2020-02-28 [1] CRAN (R 4.0.0)
#> crayon 1.3.4 2017-09-16 [1] CRAN (R 4.0.0)
#> desc 1.2.0 2018-05-01 [1] CRAN (R 4.0.0)
#> devtools 2.3.0 2020-04-10 [1] CRAN (R 4.0.0)
#> digest 0.6.25 2020-02-23 [1] CRAN (R 4.0.0)
#> ellipsis 0.3.0 2019-09-20 [1] CRAN (R 4.0.0)
#> evaluate 0.14 2019-05-28 [1] CRAN (R 4.0.0)
#> fansi 0.4.1 2020-01-08 [1] CRAN (R 4.0.0)
#> fs 1.4.1 2020-04-04 [1] CRAN (R 4.0.0)
#> glue 1.4.0 2020-04-03 [1] CRAN (R 4.0.0)
#> highr 0.8 2019-03-20 [1] CRAN (R 4.0.0)
#> htmltools 0.4.0.9003 2020-05-02 [1] Github (rstudio/htmltools@984b39c)
#> knitr 1.28 2020-02-06 [1] CRAN (R 4.0.0)
#> magrittr 1.5 2014-11-22 [1] CRAN (R 4.0.0)
#> memoise 1.1.0 2017-04-21 [1] CRAN (R 4.0.0)
#> pkgbuild 1.0.7 2020-04-25 [1] CRAN (R 4.0.0)
#> pkgload 1.0.2 2018-10-29 [1] CRAN (R 4.0.0)
#> prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.0.0)
#> processx 3.4.2 2020-02-09 [1] CRAN (R 4.0.0)
#> ps 1.3.3 2020-05-08 [1] CRAN (R 4.0.0)
#> R6 2.4.1 2019-11-12 [1] CRAN (R 4.0.0)
#> remotes 2.1.1 2020-02-15 [1] CRAN (R 4.0.0)
#> rlang 0.4.6 2020-05-02 [1] CRAN (R 4.0.0)
#> rmarkdown 2.2.0 2020-05-02 [1] Github (cpsievert/rmarkdown@310fbeb)
#> rprojroot 1.3-2 2018-01-03 [1] CRAN (R 4.0.0)
#> sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 4.0.0)
#> stringi 1.4.6 2020-02-17 [1] CRAN (R 4.0.0)
#> stringr 1.4.0 2019-02-10 [1] CRAN (R 4.0.0)
#> testthat 2.3.2 2020-03-02 [1] CRAN (R 4.0.0)
#> usethis 1.6.0 2020-04-09 [1] CRAN (R 4.0.0)
#> withr 2.2.0 2020-04-20 [1] CRAN (R 4.0.0)
#> xfun 0.13 2020-04-13 [1] CRAN (R 4.0.0)
#> yaml 2.2.1 2020-02-01 [1] CRAN (R 4.0.0)
#>
#> [1] C:/Users/john/Documents/R/win-library/4.0
#> [2] C:/Program Files/R/R-4.0.0/library
I always commit everything in site_libs/ in order to keep the website functioning. Thus I'd also recommend you commit everything in site_libs/, even if it seems unnecessary.