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Create a Bug Tracking System Early and Not Often
The earlier people get used to using a bug tracking system the better. If you are 3/4 through a project and then install a bug tracking system it won't be used. You need to install a bug tracking system early so people will use it.
Programmers generally resist bug tracking, yet when used correctly it can really help a project:
Problems aren't dropped on the floor.
Problems are automatically routed to responsible individuals.
The lifecycle of a problem is tracked so people can argue back and forth with good information.
Managers can make the big schedule and staffing decisions based on the number of and types of bugs in the system.
Configuration management has a hope of matching patches back to the problems they fix.
QA and technical support have a communication medium with developers.
Not sexy things, just good solid project improvements.
FYI, it's not a good idea to reward people by the number of bugs they fix :-)
Source code control should be linked to the bug tracking system. During the part of a project where source is frozen before a release only checkins accompanied by a valid bug ID should be accepted. And when code is changed to fix a bug the bug ID should be included in the checkin comments.
Sources
Several projects have found DDTS a workable system (I 've not verified this link for this PHP release, DDTS may not work for PHP). There is also a GNU bug tracking system available. Roll your own is a popular option but using an existing system seems more cost efficient.
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Honor Responsibilities
Responsibility for software modules is scoped. Modules are either the responsibility of a particular person or are common. Honor this division of responsibility. Don't go changing things that aren't your responsibility to change. Only mistakes and hard feelings will result.