Q: What is the Master Password dialog, and can I suppress it?
NetBeans frequently needs to store various kinds of passwords - to databases, bug tracking systems, and so on. It is insecure to save these to disk, so as of NetBeans 6.9 the IDE tries to use your operating system's native facility to store passwords. This could be login-based encryption on Windows; the Keychain on Mac OS X; or GNOME Keyring or KWallet on Linux or Solaris.
Under some conditions, there can be problems accessing the native keyring. Perhaps you are using an unsupported platform (such as Linux with an unusual desktop system), or perhaps there is just some other error opening the keyring. (Adding -J-Dorg.netbeans.modules.keyring.level=FINE to <tt>etc/netbeans.conf will add information to your log file about the problem with the native keyring, as well as information about which passwords the IDE was trying to load or store. You are encouraged to file bug reports about these cases since they might be fixable.)
In such cases the IDE behaves like Firefox and similar applications - it falls back to saving your passwords in encrypted form in your user directory and decrypting them with a "master password" which is prompted for once per IDE session and never saved. Pick a master password when first prompted (it should be as secure as your most sensitive normal password), and enter it on subsequent runs. If you forget it, you can set a new master password but any passwords encrypted with the old one will be discarded.
As of NetBeans 7.0, you can set -J-Dnetbeans.keyring.no.master=true in etc/netbeans.conf. In this case, when native keyring integration fails, an in-memory-only keyring will be used: any passwords obtained by various parts of the IDE will be remembered for the duration of the IDE session but forgotten when you shut down the program. Generally this will be worse than using a master password because you may have to enter multiple regular passwords in a single session.
There is no option to store passwords in cleartext. (NetBeans 6.8 would in some cases persist passwords and other cases forget them after a restart.)