To force LF line endings for all text files, you can create .gitattributes file in top-level of your repository with the following lines (change as desired):
# Ensure all C and PHP files use LF.
*.c         eol=lf
*.php       eol=lf
which ensures that all files that Git considers to be text files have normalized (LF) line endings in the repository (normally core.eol configuration controls which one do you have by default).
Based on the new attribute settings, any text files containing CRLFs should be normalized by Git. If this won't happen automatically, you can refresh a repository manually after changing line endings, so you can re-scan and commit the working directory by the following steps (given clean working directory):
$ echo "* text=auto" >> .gitattributes
$ rm .git/index     # Remove the index to force Git to
$ git reset         # re-scan the working directory
$ git status        # Show files that will be normalized
$ git add -u
$ git add .gitattributes
$ git commit -m "Introduce end-of-line normalization"
or as per GitHub docs:
git add . -u
git commit -m "Saving files before refreshing line endings"
git rm --cached -r . # Remove every file from Git's index.
git reset --hard # Rewrite the Git index to pick up all the new line endings.
git add . # Add all your changed files back, and prepare them for a commit.
git commit -m "Normalize all the line endings" # Commit the changes to your repository.
See also: @Charles Bailey post.
In addition, if you would like to exclude any files to not being treated as a text, unset their text attribute, e.g.
manual.pdf      -text
Or mark it explicitly as binary:
# Denote all files that are truly binary and should not be modified.
*.png binary
*.jpg binary
To see some more advanced git normalization file, check .gitattributes at Drupal core:
# Drupal git normalization
# @see https://www.kernel.org/pub/software/scm/git/docs/gitattributes.html
# @see https://www.drupal.org/node/1542048
# Normally these settings would be done with macro attributes for improved
# readability and easier maintenance. However macros can only be defined at the
# repository root directory. Drupal avoids making any assumptions about where it
# is installed.
# Define text file attributes.
# - Treat them as text.
# - Ensure no CRLF line-endings, neither on checkout nor on checkin.
# - Detect whitespace errors.
#   - Exposed by default in `git diff --color` on the CLI.
#   - Validate with `git diff --check`.
#   - Deny applying with `git apply --whitespace=error-all`.
#   - Fix automatically with `git apply --whitespace=fix`.
*.config  text eol=lf whitespace=blank-at-eol,-blank-at-eof,-space-before-tab,tab-in-indent,tabwidth=2
*.css     text eol=lf whitespace=blank-at-eol,-blank-at-eof,-space-before-tab,tab-in-indent,tabwidth=2
*.dist    text eol=lf whitespace=blank-at-eol,-blank-at-eof,-space-before-tab,tab-in-indent,tabwidth=2
*.engine  text eol=lf whitespace=blank-at-eol,-blank-at-eof,-space-before-tab,tab-in-indent,tabwidth=2 diff=php
*.html    text eol=lf whitespace=blank-at-eol,-blank-at-eof,-space-before-tab,tab-in-indent,tabwidth=2 diff=html
*.inc     text eol=lf whitespace=blank-at-eol,-blank-at-eof,-space-before-tab,tab-in-indent,tabwidth=2 diff=php
*.install text eol=lf whitespace=blank-at-eol,-blank-at-eof,-space-before-tab,tab-in-indent,tabwidth=2 diff=php
*.js      text eol=lf whitespace=blank-at-eol,-blank-at-eof,-space-before-tab,tab-in-indent,tabwidth=2
*.json    text eol=lf whitespace=blank-at-eol,-blank-at-eof,-space-before-tab,tab-in-indent,tabwidth=2
*.lock    text eol=lf whitespace=blank-at-eol,-blank-at-eof,-space-before-tab,tab-in-indent,tabwidth=2
*.map     text eol=lf whitespace=blank-at-eol,-blank-at-eof,-space-before-tab,tab-in-indent,tabwidth=2
*.md      text eol=lf whitespace=blank-at-eol,-blank-at-eof,-space-before-tab,tab-in-indent,tabwidth=2
*.module  text eol=lf whitespace=blank-at-eol,-blank-at-eof,-space-before-tab,tab-in-indent,tabwidth=2 diff=php
*.php     text eol=lf whitespace=blank-at-eol,-blank-at-eof,-space-before-tab,tab-in-indent,tabwidth=2 diff=php
*.po      text eol=lf whitespace=blank-at-eol,-blank-at-eof,-space-before-tab,tab-in-indent,tabwidth=2
*.profile text eol=lf whitespace=blank-at-eol,-blank-at-eof,-space-before-tab,tab-in-indent,tabwidth=2 diff=php
*.script  text eol=lf whitespace=blank-at-eol,-blank-at-eof,-space-before-tab,tab-in-indent,tabwidth=2
*.sh      text eol=lf whitespace=blank-at-eol,-blank-at-eof,-space-before-tab,tab-in-indent,tabwidth=2 diff=php
*.sql     text eol=lf whitespace=blank-at-eol,-blank-at-eof,-space-before-tab,tab-in-indent,tabwidth=2
*.svg     text eol=lf whitespace=blank-at-eol,-blank-at-eof,-space-before-tab,tab-in-indent,tabwidth=2
*.theme   text eol=lf whitespace=blank-at-eol,-blank-at-eof,-space-before-tab,tab-in-indent,tabwidth=2 diff=php
*.twig    text eol=lf whitespace=blank-at-eol,-blank-at-eof,-space-before-tab,tab-in-indent,tabwidth=2
*.txt     text eol=lf whitespace=blank-at-eol,-blank-at-eof,-space-before-tab,tab-in-indent,tabwidth=2
*.xml     text eol=lf whitespace=blank-at-eol,-blank-at-eof,-space-before-tab,tab-in-indent,tabwidth=2
*.yml     text eol=lf whitespace=blank-at-eol,-blank-at-eof,-space-before-tab,tab-in-indent,tabwidth=2
# Define binary file attributes.
# - Do not treat them as text.
# - Include binary diff in patches instead of "binary files differ."
*.eot     -text diff
*.exe     -text diff
*.gif     -text diff
*.gz      -text diff
*.ico     -text diff
*.jpeg    -text diff
*.jpg     -text diff
*.otf     -text diff
*.phar    -text diff
*.png     -text diff
*.svgz    -text diff
*.ttf     -text diff
*.woff    -text diff
*.woff2   -text diff
See also: