git is ignoring files that aren't in .gitignore?

Solved: Decided to delete the .git directory and try again, since there was nothing in it anyway. rm -rf .git, then git init, then git add .. Now it's working, everything is getting added correctly, and things that should be ignored are. Think I mis-cloned 960gs or html5boilerplate into the project directory instead of a subdirectory. Thanks everyone for your replies, much appreciated.

There are lots of questions on SO about git failing to ignore files specified in .gitignore. My problem is the exact opposite - git is ignoring files that aren't listed in .gitignore.

For example, I've just started a web project using HTML5Boilerplate and 960 Grid System, and am trying to do the initial commit. However, only a few of the files and directories I need are being staged when I run 'git add *'.

.gitignore in the project directory specifies a list of project, vcs, and other files to ignore, but not *.html, *.xml, *.conf, .htaccess, *.ico, *.png files, which are not being staged to the index. Strangely, one html file is being added, demo.html, while index.html isn't.

Anyone have any idea what's wrong and how to fix it?

Here's a transcript of the operations for clarity:

%> ls -al
total 136
drwxr-xr-x 13 me me  4096 2010-11-08 14:04 .
drwxr-xr-x  6 me me  4096 2010-11-08 13:23 ..
-rw-r--r--  1 me me   720 2010-11-08 13:21 404.html
-rw-r--r--  1 me me  1893 2010-11-08 13:21 apple-touch-icon.png
drwxr-xr-x  3 me me  4096 2010-11-08 13:21 build
-rw-r--r--  1 me me   802 2010-11-08 13:21 crossdomain.xml
drwxr-xr-x  3 开发者_如何学Cme me  4096 2010-11-08 13:24 css
drwxr-xr-x  2 me me  4096 2010-11-08 13:21 demo
-rwxr-xr-x  1 me me  8920 2010-11-08 13:15 demo.html
-rw-r--r--  1 me me  1150 2010-11-08 13:21 favicon.ico
drwxr-xr-x  8 me me  4096 2010-11-08 14:04 .git
-rw-r--r--  1 me me   266 2010-11-08 13:44 .gitignore
-rw-r--r--  1 me me  8011 2010-11-08 13:21 .htaccess
drwxr-xr-x  2 me me  4096 2010-11-08 13:21 images
drwxr-xr-x  2 me me  4096 2010-11-08 13:15 img
-rw-r--r--  1 me me  3115 2010-11-08 13:21 index.html
drwxr-xr-x  5 me me  4096 2010-11-08 13:21 js
-rw-r--r--  1 me me  5166 2010-11-08 13:21 lighttpd.conf
-rw-r--r--  1 me me  3484 2010-11-08 13:21 mime.types
-rw-r--r--  1 me me  3413 2010-11-08 13:21 nginx.conf
-rw-r--r--  1 me me     0 2010-11-08 14:04 output.txt
-rw-r--r--  1 me me  6277 2010-11-08 13:21 README.markdown
-rw-r--r--  1 me me   107 2010-11-08 13:21 robots.txt
drwxr-xr-x  4 me me  4096 2010-11-08 13:17 templates
drwxr-xr-x  3 me me  4096 2010-11-08 13:21 test
drwxr-xr-x  2 me me  4096 2010-11-08 13:45 vim~
-rw-r--r--  1 me me 12274 2010-11-08 13:21 web.config
drwxr-xr-x  2 me me  4096 2010-11-08 12:09 wireframes

%> less .gitignore
# Numerous always-ignore extensions
*.diff
*.err
*.orig
*.log
*.rej
*.swo
*.swp
*.vi
*~

# OS or Editor folders
.DS_Store
.cache
.project
.settings
nbproject
thumb.db

# Folders to ignore
.hg
.svn
publish
.idea
templates
template

# files
build/buildinfo.properties

%> git add *
# Not currently on any branch.
# Changes to be committed:
#   (use "git reset HEAD <file>..." to unstage)
#
#   new file:   css/960.css
#   new file:   css/960_24_col.css
#   new file:   css/reset.css
#   new file:   css/rtl_960.css
#   new file:   css/rtl_960_24_col.css
#   new file:   css/rtl_text.css
#   new file:   css/text.css
#   new file:   css/uncompressed/960.css
#   new file:   css/uncompressed/960_24_col.css
#   new file:   css/uncompressed/demo.css
#   new file:   css/uncompressed/reset.css
#   new file:   css/uncompressed/rtl_960.css
#   new file:   css/uncompressed/rtl_960_24_col.css
#   new file:   css/uncompressed/rtl_text.css
#   new file:   css/uncompressed/text.css
#   new file:   demo.html
#   new file:   img/12_col.gif
#   new file:   img/16_col.gif
#   new file:   img/24_col.gif
#   new file:   wireframes/basalmiq01.pdf
#   new file:   wireframes/basalmiq01.png
#   new file:   wireframes/basalmiq01.xml
#   new file:   wireframes/fcf_mockingbird.zip
#   new file:   wireframes/fcf_mockingbird_.zip
#
# Changed but not updated:
#   (use "git add <file>..." to update what will be committed)
#   (use "git checkout -- <file>..." to discard changes in working directory)
#
#   modified:   .gitignore
#
# Untracked files:
#   (use "git add <file>..." to include in what will be committed)
#
#   output.txt

Maybe those files are already controlled by git.