Why did running `git pull` remove my committed changes?

Question

According to the documentation on git, a git pull will perform a fetch of the current branch and then run a git merge to merge the changes. After a colleague committed and pushed his changes to the server, I went to retrieve them.

First, I committed changes that I had:

git add src
git add war

Running git status confirmed that my changes were staged to be committed. Next, I ran:

git commit -m "Another commit to work on scrolling"

Afterwards, I pulled down changes:

git pull

This showed me some warnings:

remote: Counting objects: 31, done.
remote: Compressing objects: 100% (16/16), done.
remote: Total 16 (delta 13), reused 3 (delta 0)
Unpacking objects: 100% (16/16), done.
From github.com:FullCreative/Loop
 + 3f00b3f...2e09a49 master     -> master  (forced update)
Warning: fetch updated the current branch head.
Warning: fast-forwarding your working tree from
Warning: commit 3f00b3f6cb6ed6beddb16baa92f1beaa82b6944c.
Already up-to-date.

Lastly, I pushed my changes -- or rather tried to push them -- to the server:

git push

Question:

Now, why did this remove all of my changes? Even files that my colleague didn't modify were removed from my working directory.

Console Output:

For thoroughness, below is the console log from my terminal. This shows the commands I ran, and the output from those commands:

jem@jem-VPCF136FM:~$ cd git
jem@jem-VPCF136FM:~/git$ l
Loop/  Loop-1-18.tar.gz
jem@jem-VPCF136FM:~/git$ cd Loop
jem@jem-VPCF136FM:~/git/Loop$ l
Loop/  README  readme.textile
jem@jem-VPCF136FM:~/git/Loop$ l
Loop/  README  readme.textile
jem@jem-VPCF136FM:~/git/Loop$ cd Loop
jem@jem-VPCF136FM:~/git/Loop/Loop$ l
src/  war/
jem@jem-VPCF136FM:~/git/Loop/Loop$ git add src
jem@jem-VPCF136FM:~/git/Loop/Loop$ git status
# On branch master
# Changes to be committed:
#   (use "git reset HEAD <file>..." to unstage)
#
#   modified:   src/com/fullcreative/loop/Globals.java
#   modified:   src/com/fullcreative/loop/LoopController.java
#   modified:   src/com/fullcreative/loop/LoopDao.java
#   modified:   src/com/fullcreative/loop/LoopDaoJdo.java
#   modified:   src/com/fullcreative/loop/LoopService.java
#   new file:   src/com/fullcreative/loop/TestLoopController.java
#
# Changes not staged for commit:
#   (use "git add <file>..." to update what will be committed)
#   (use "git checkout -- <file>..." to discard changes in working directory)
#
#   modified:   war/WEB-INF/LoopDispatcher-servlet.xml
#   modified:   war/WEB-INF/appengine-web.xml
#   modified:   war/WEB-INF/applicationContext-security.xml
#   modified:   war/WEB-INF/html/index.html
#   modified:   war/WEB-INF/web.xml
#   modified:   war/js/loop.js
#
# Untracked files:
#   (use "git add <file>..." to include in what will be committed)
#
#   war/WEB-INF/admin/local-storage.html
jem@jem-VPCF136FM:~/git/Loop/Loop$ git add war
jem@jem-VPCF136FM:~/git/Loop/Loop$ git status
# On branch master
# Changes to be committed:
#   (use "git reset HEAD <file>..." to unstage)
#
#   modified:   src/com/fullcreative/loop/Globals.java
#   modified:   src/com/fullcreative/loop/LoopController.java
#   modified:   src/com/fullcreative/loop/LoopDao.java
#   modified:   src/com/fullcreative/loop/LoopDaoJdo.java
#   modified:   src/com/fullcreative/loop/LoopService.java
#   new file:   src/com/fullcreative/loop/TestLoopController.java
#   modified:   war/WEB-INF/LoopDispatcher-servlet.xml
#   new file:   war/WEB-INF/admin/local-storage.html
#   modified:   war/WEB-INF/appengine-web.xml
#   modified:   war/WEB-INF/applicationContext-security.xml
#   modified:   war/WEB-INF/html/index.html
#   modified:   war/WEB-INF/web.xml
#   modified:   war/js/loop.js
#
jem@jem-VPCF136FM:~/git/Loop/Loop$ git commit -m "Another commit to work on scolling"
[master 3f00b3f] Another commit to work on scolling
 13 files changed, 726 insertions(+), 218 deletions(-)
 create mode 100644 Loop/src/com/fullcreative/loop/TestLoopController.java
 create mode 100644 Loop/war/WEB-INF/admin/local-storage.html
jem@jem-VPCF136FM:~/git/Loop/Loop$ git pull
remote: Counting objects: 31, done.
remote: Compressing objects: 100% (16/16), done.
remote: Total 16 (delta 13), reused 3 (delta 0)
Unpacking objects: 100% (16/16), done.
From github.com:FullCreative/Loop
 + 3f00b3f...2e09a49 master     -> master  (forced update)
Warning: fetch updated the current branch head.
Warning: fast-forwarding your working tree from
Warning: commit 3f00b3f6cb6ed6beddb16baa92f1beaa82b6944c.
Already up-to-date.
jem@jem-VPCF136FM:~/git/Loop/Loop$ git push
Everything up-to-date
jem@jem-VPCF136FM:~/git/Loop/Loop$ git status
# On branch master
nothing to commit (working directory clean)
jem@jem-VPCF136FM:~/git/Loop/Loop$ git history
git: 'history' is not a git command. See 'git --help'.
jem@jem-VPCF136FM:~/git/Loop/Loop$ git --help
usage: git [--version] [--exec-path[=<path>]] [--html-path]
       [-p|--paginate|--no-pager] [--no-replace-objects]
       [--bare] [--git-dir=<path>] [--work-tree=<path>]
       [-c name=value] [--help]
       <command> [<args>]

The most commonly used git commands are:
   add        Add file contents to the index
   bisect     Find by binary search the change that introduced a bug
   branch     List, create, or delete branches
   checkout   Checkout a branch or paths to the working tree
   clone      Clone a repository into a new directory
   commit     Record changes to the repository
   diff       Show changes between commits, commit and working tree, etc
   fetch      Download objects and refs from another repository
   grep       Print lines matching a pattern
   init       Create an empty git repository or reinitialize an existing one
   log        Show commit logs
   merge      Join two or more development histories together
   mv         Move or rename a file, a directory, or a symlink
   pull       Fetch from and merge with another repository or a local branch
   push       Update remote refs along with associated objects
   rebase     Forward-port local commits to the updated upstream head
   reset      Reset current HEAD to the specified state
   rm         Remove files from the working tree and from the index
   show       Show various types of objects
   status     Show the working tree status
   tag        Create, list, delete or verify a tag object signed with GPG

See 'git help <command>' for more information on a specific command.
jem@jem-VPCF136FM:~/git/Loop/Loop$ git log
commit 2e09a498829e2b12e4bbdff8f8c39c2ce47dacb7
Author: Josh Iwata < [email protected]>
Date:   Thu Mar 15 14:25:28 2012 -0700

    Design revamp

commit 2927f853041dab06a48861498adc945d6969865a
Author: James Mortensen <[email protected]>
Date:   Wed Mar 14 09:25:46 2012 -0700

    Removed Alert.

commit 07deceb9cb3cda6b913b2bde96970682ecdbddb7
Author: James Mortensen <[email protected]>
Date:   Wed Mar 14 09:04:12 2012 -0700

    Added url pattern to the servlet to get rid of the error.

commit f2d48bb735e5c3f1d3cb88ad80483e5596aaa063
Author: James Mortensen <[email protected]>
Date:   Tue Mar 13 15:44:28 2012 -0700

    iJames took over again!

commit 88fb39c0b37b2dfc5a13e30f212cba525e33f531
Author: David Raffauf <[email protected]>
Date:   Tue Mar 13 15:42:26 2012 -0700

    I test update

commit 5b1af15d166fc766a1a892a13865d9c5be506a6f
Author: Josh Iwata < [email protected]>
jem@jem-VPCF136FM:~/git/Loop/Loop$ git status
# On branch master
nothing to commit (working directory clean)
jem@jem-VPCF136FM:~/git/Loop/Loop$ git pull
Already up-to-date.
jem@jem-VPCF136FM:~/git/Loop/Loop$ l
src/  war/
jem@jem-VPCF136FM:~/git/Loop/Loop$ cd src
jem@jem-VPCF136FM:~/git/Loop/Loop/src$ l
cacerts.bin  com/  log4j.properties  META-INF/
jem@jem-VPCF136FM:~/git/Loop/Loop/src$ cd com
jem@jem-VPCF136FM:~/git/Loop/Loop/src/com$ l
fullcreative/
jem@jem-VPCF136FM:~/git/Loop/Loop/src/com$ cd fullcreative/loop/
jem@jem-VPCF136FM:~/git/Loop/Loop/src/com/fullcreative/loop$ l
AbstractBaseController.java   Comment.java                    LoopController.java     PusheableResponse.java
AccountController.java        EmailService.java               LoopDao.java            samples/
Account.java                  EnvironmentService.java         LoopDaoJdo.java         security/
AccountService.java           FormManagerController.java      Loop.java               Settings.java
AuthenticatorController.java  Globals.java                    LoopService.java        TagSubscription.java
AuthenticatorService.java     GoogleCometChannelService.java  LoopServlet.java        UserDao.java
Cacheable.java                HttpRequestHandler.java         Memcached.java          UserDaoJdo.java
Card.java                     InvitationDetailsDaoJdo.java    OAuth2User.java         User.java
CardManagerController.java    InvitationDetails.java          OAuth2UserService.java
CardTemplateService.java      JSONPResponse.java              PMF.java
jem@jem-VPCF136FM:~/git/Loop/Loop/src/com/fullcreative/loop$ cd /
jem@jem-VPCF136FM:/$ cd 
jem@jem-VPCF136FM:~$ cd workspace
jem@jem-VPCF136FM:~/workspace$ l
ActiveResponseWebService/          ConversionChromeApp.pem      GAE Spring Security/       LoopSVN/
Adaptiv3ChatDemo/                  ConversionChromeExtension/   GAE Spring Security Demo/  Loop.tar.gz
Adaptiv3ChatDemo-2.zip             ConversionSupportChromeApp/  gdata-samples-read-only/   ReverseProxyDemo/
Adaptiv3ChatDemo.zip               ConversionSupportLive/       LexLegal/                  rhino-for-webapps-demo/
AmazonC3Demo/                      ConversionSupportLiveNew/    LexMatter/                 SB4.0/
App-AnswerConnect/                 ConversionSupportLiveNew2/   local_db.bin               SB4.0_branch/
appengine-java-sdk-1.6.2.1/        ConversionSupportLive.zip    Loop/                      sokolove_lawfirm/
appengine-java-sdk-1.6.2.1.zip     Conversion Support- Mobile/  Loop2/                     test/
appengine-java-sdk-1.6.3.1/        ConversionSupportWebsite/    Loop-Oauth2-Demo/          Test/
appengine-java-sdk-1.6.3.1.zip     ConverstionSupportMobileV1/  LoopRepo/                  Thinclient-c3/
AppointmentSchedulingAppGAEJ/      ConverstionSupportMobileV2/  LoopRepo-1-12-2-.tar.gz    Thinclient-c3.zip
ChatClientWebservices/             datastore-indexes-auto.xml   LoopRepo1-12.tar.gz
ContactManagementSystemDataStore/  EchopassChatClient/          LoopRepo1-13.tar.gz
ConversionChromeApp0.1.1109.6.crx  FullTextSearchService/       LoopRepo.tar.gz
jem@jem-VPCF136FM:~/workspace$ cd Loop
jem@jem-VPCF136FM:~/workspace/Loop$ l
Loop/  README  readme.textile
jem@jem-VPCF136FM:~/workspace/Loop$ cd Loop
jem@jem-VPCF136FM:~/workspace/Loop/Loop$ l
src/  war/
jem@jem-VPCF136FM:~/workspace/Loop/Loop$ cd src
jem@jem-VPCF136FM:~/workspace/Loop/Loop/src$ l
cacerts.bin  com/  log4j.properties  META-INF/
jem@jem-VPCF136FM:~/workspace/Loop/Loop/src$ cd com
jem@jem-VPCF136FM:~/workspace/Loop/Loop/src/com$ l
fullcreative/
jem@jem-VPCF136FM:~/workspace/Loop/Loop/src/com$ cd fullcreative/
jem@jem-VPCF136FM:~/workspace/Loop/Loop/src/com/fullcreative$ l
loop/
jem@jem-VPCF136FM:~/workspace/Loop/Loop/src/com/fullcreative$ cd loop
jem@jem-VPCF136FM:~/workspace/Loop/Loop/src/com/fullcreative/loop$ 
jem@jem-VPCF136FM:~/workspace/Loop/Loop/src/com/fullcreative/loop$ l
AccountController.java        Card.java                     LoopController.java  Memcached.java          UserDao.java
Account.java                  Comment.java                  LoopDao.java         OAuth2User.java         UserDaoJdo.java
AccountService.java           EnvironmentService.java       LoopDaoJdo.java      OAuth2UserService.java  User.java
AuthenticatorController.java  HttpRequestHandler.java       Loop.java            PMF.java
AuthenticatorService.java     InvitationDetailsDaoJdo.java  LoopService.java     samples/
Cacheable.java                InvitationDetails.java        LoopServlet.java     security/
jem@jem-VPCF136FM:~/workspace/Loop/Loop/src/com/fullcreative/loop$ cd ../../../../
jem@jem-VPCF136FM:~/workspace/Loop/Loop$ cd ../../..
jem@jem-VPCF136FM:~$ cd git
jem@jem-VPCF136FM:~/git$ l
Loop/  Loop-1-18.tar.gz
jem@jem-VPCF136FM:~/git$ cd Loop
jem@jem-VPCF136FM:~/git/Loop$ l
Loop/  README  readme.textile
jem@jem-VPCF136FM:~/git/Loop$ cd Loop
jem@jem-VPCF136FM:~/git/Loop/Loop$ l
src/  war/
jem@jem-VPCF136FM:~/git/Loop/Loop$ 

UPDATE:

I can access my commits by checking out from the hash:

git checkout 3f00b3f6cb6ed6beddb16baa92f1beaa82b6944c

So why aren't these included in my push to the server?

UPDATE #2

Results of git reflog:

3f00b3f HEAD@{0}: checkout: moving from master to 3f00b3f6cb6ed6beddb16baa92f1beaa82b6944c
2e09a49 HEAD@{1}: checkout: moving from 3f00b3f6cb6ed6beddb16baa92f1beaa82b6944c to master
3f00b3f HEAD@{2}: checkout: moving from master to 3f00b3f6cb6ed6beddb16baa92f1beaa82b6944c
2e09a49 HEAD@{3}: pull : forced-update
3f00b3f HEAD@{4}: commit: Another commit to work on scolling
2927f85 HEAD@{5}: commit: Removed Alert.
07deceb HEAD@{6}: commit: Added url pattern to the servlet to get rid of the error.
f2d48bb HEAD@{7}: commit: iJames took over again!
88fb39c HEAD@{8}: pull : fast-forward
a22893e HEAD@{9}: commit: Committing a very important change to intro.css. Not!
ac19755 HEAD@{10}: pull : fast-forward
d2a401d HEAD@{11}: commit: This is a test
85a6328 HEAD@{12}: commit: Modified gitignore yet again.
251f557 HEAD@{13}: commit: Committing the classpath. Hope it works.
4e7a428 HEAD@{14}: checkout: moving from local_master to master
97aa2d7 HEAD@{15}: checkout: moving from master to local_master
4e7a428 HEAD@{16}: commit: Added Admin panel for making system changes. Modified the title and description so they go into edit 
38dc2fa HEAD@{17}: commit: Added notifications and real time comet.
bc2f950 HEAD@{18}: commit: Real time updates and chrome notifications.
bc2f950 HEAD@{19}: commit: Adding TagSubscription class.
5e696f4 HEAD@{20}: commit: Bulk delete, fixed delete bug, tagging features and subscriptions. Added more server-side caching. Ad
7b41cc2 HEAD@{21}: commit: adding dropdown plugin files
d9e3716 HEAD@{22}: commit: Added filter list to top, made dynamic, and deployed to 2-20.
e256d21 HEAD@{23}: commit: Cleaned up the HTML code.
d9e3716 HEAD@{24}: commit: Third time is a charm.
3e0863f HEAD@{25}: commit: Here is the 2nd commit for tag-it.
13e70c8 HEAD@{26}: commit: Added the tag-it tags to the application and connected to the database.
0893615 HEAD@{27}: commit: Deployed 2-7 and made default version.
0073e04 HEAD@{28}: commit: Deployed to 2-7 and made the default version.  Finalized mobile form, although the error class shadow
0073e04 HEAD@{29}: commit: test
4351a93 HEAD@{30}: commit: Added notifications for comments and cleaned up mobile form.
5674cfb HEAD@{31}: commit: Added Developer API call to switch users for @loopround.com users.
a22808f HEAD@{32}: commit: updating
8fa1a39 HEAD@{33}: commit: updating the repository
8fa1a39 HEAD@{34}: commit: Deployed to http://0-9-2012-1-27.loopaback.appspot.com/
4786be1 HEAD@{35}: commit: Updating the inbox counts on each loop on page load. Also changed the style of the inbox count on the
33bf8d5 HEAD@{36}: commit: Adding elastic JS library.
095d8e6 HEAD@{37}: commit: Hooked up inbox counts and colors on the loops.
d3275ef HEAD@{38}: commit: committing.
a66024c HEAD@{39}: commit: Put in place email notifications for sharing. Put in place more logging statements to catch errors. F
a66024c HEAD@{40}: commit: Fixed sharing settings and cleaned up some of the code. Fixed the invitation system and also added so
e87ca75 HEAD@{41}: commit: Fixed sharing settings and cleaned up some of the code. Fixed the invitation system and also added so
e87ca75 HEAD@{42}: commit: Got rid of login form and also integrated Loop feedback form.
b2d7da9 HEAD@{43}: commit: Eliminated the login page and also integrated the Feedback Loop Form.
b2d7da9 HEAD@{44}: commit: Added the Loop Form.
e7ea0eb HEAD@{45}: commit: Added the Loop Form to the Loop Application and connected it to the services.
e7ea0eb HEAD@{46}: commit: Trying to get all the files for the settings page in the repo.
97aa2d7 HEAD@{47}: commit: test
36d4841 HEAD@{48}: commit: Got the settings page in place so users can be added and removed.
cf83cbd HEAD@{49}: commit: Committing this file because I want it to accept changes, not have the repository just simply force m
e7ccb2d HEAD@{50}: commit: Merged Josh's changes, I hope!
90ee5a5 HEAD@{51}: commit: Merged Josh's changes. Why I have to do this manually, I don't know?
3fc14b4 HEAD@{52}: commit: Service giving ability to send email to a user.
2ce4a6c HEAD@{53}: commit: Worked on the UI for adding a user to a Loop. Also fixed the display so it shows all active users ass
21caa9b HEAD@{54}: commit: Updated the application-manifest.xml file with the new LoopRound name and latest version info.
4330694 HEAD@{55}: commit: Deployed to http://0-9-2012-1-12-1715.loopaback.appspot.com/# and made the default version. Added in 
adde3cd HEAD@{56}: commit: Can now add new loops from the Loop screen. To rename the loop or access it's settings page; currentl
6902710 HEAD@{57}: commit: Settings page is functional to edit the loop name.
6980c79 HEAD@{58}: merge branch 'master' of [email protected]:FullCreative/Loop.git: Fast-forward
e364173 HEAD@{59}: commit: Added Josh's CSS to style.css. 2nd attempt.
0e464f1 HEAD@{60}:

.git/config file

[core]
    repositoryformatversion = 0
    filemode = true
    logallrefupdates = true
    autocrlf = false
[remote "origin"]
    url = [email protected]:FullCreative/Loop.git
    fetch = +refs/heads/*:refs/heads/*
    push = refs/heads/*:refs/heads/*
[branch "master"]
    remote = origin
    merge = refs/heads/master

Answer 1

The following lines look suspicious:

From github.com:FullCreative/Loop
 + 3f00b3f...2e09a49 master     -> master  (forced update)
Warning: fetch updated the current branch head.
Warning: fast-forwarding your working tree from
Warning: commit 3f00b3f6cb6ed6beddb16baa92f1beaa82b6944c.

In particular, if you are configured correctly, the line should indicate master -> origin/master, or whatever the name of your remote is. Instead, it reads master -> master. This indicates that the master branch on the remote is being written directly to the master branch in your local repo; which means that you lose the reference to your commit (though as you noticed, it's still in your repo, it's just not referenced by anything). This is why git printed "Warning: fetch updated the current branch head."

Check your .git/config. It should contain something like:

[remote "origin"]
        url = <some url>
        fetch = +refs/heads/*:refs/remotes/origin/*

However, based on the error you got, it probably contains something like:

[remote "origin"]
        url = <some url>
        fetch = +refs/heads/*:refs/heads/*

This tells git that when fetching, it should write the value of the remote branch directly to your local branch. Normally, in the above correct configuration, when you fetch a remote ref, it is written to refs/remotes/<remote>/<name>. This allows you to have keep track of both the upstream commit, and your local commit, so that you can merge them. In the incorrect configuration, you are simply overwriting your local ref, losing track of what you had there originally.

I'm not sure how you got set up this way; perhaps you did something like git clone --mirror or git remote add --mirror=fetch. Regardless, you can manually edit your .git/config file, and correct the fetch line as indicated above.

Answer 2

I think the key to the problem lies in the ominous message on your pull command: see where it says "forced update"? That's Git's slightly obscure way of telling you that the branch (master) has been been either re-created or rebased, a big no-no on a shared repository.

You should ask the other collaborators if they rebased or re-created master. If you want a pictorial view of what happened, try gitk --all.

There's probably no great way to solve your problem, but the easy thing to do is cherry-pick that one commit on master (git cherry-pick 3f00b3f) and push again.