Software Version Controlling Best Practices

Always use version controlling
Use version controlling/source control even if one developer exists. This issue brings change tracking and versioning of the application continuously. For multi developers, it brings more benefits like co-working on same files and fast codebase updates.

Do not commit halfdone work
Each commit should consist of a complete task (issue, bugfix, etc.). Partial commits may cause unfunctionality, crash of application or even compilation errors.

Full Update -> Build -> Run -> Full Commit rule

For having no trouble, a stable version controlling process should be applied. According to this process, you should full update the code, then build and run your application. If application runs correctly, you should commit all of your updated files. While committing, inspect all of your changed files and changes. If all team members apply this process, application will always continue to run and no one will prevent others work. 

Commit atomicity/granularity

Do not use version controlling system to backup each single file separately and do not commit hundreds of files after days or weeks of development. Commits should be atomic, and as a best practice, should include files which are related with only one task. Late commits also brings more conflicts.

Use descriptive commit messages

Commit messages are important for tracking changes. Descriptive commit messages help developers to control old versions of code within a functional context, instead of date and time only.

Don't commit generated files

Use "ignore" funcionalities of your version controlling tool to ignore commiting and updating of generated files (e.g. target folders, user settings, IDE generated files, generated classes after each build etc.) By doing this, you will not waste your time for managing those unstable/unimportant files.

Continuous integration

Use continuous integration along with version controlling. By doing that, perform automated builds and deploys to a specific location. Also, configure the tool to create a separate version number (with a predefined versioning algorithm, e.g. <major_changes>.<minor_changes>.<bug_fixes>) for each build. This will be useful to trace tests and deployments.

Use qualified version controlling tools and plugins (especially for merge)

Version controlling tool quality is also important. It must at least show changed files clearly, give ability to merge conflicted files easily and view old versions of files. Besides, it will be better to have a branching function to manage versions and and issue tracking system synchronization to manage issue-related code file matchings.

Use branches for testing and different lines of code

You should use different code branches for development, testing and also production. If a version of code is being tested, development should not continue on that branch. Development can continue on another branch and when a new version will be tested after fixing some bugs and adding new properties, a new test branch should be provided with a new version. When a stable test branch is reached, it may be released as a production branch.

You can also take a look at the below link for version controlling basics:
http://betterexplained.com/articles/a-visual-guide-to-version-control/