Ubuntu – What are dot-files

.local, .cache, and .config are part of the FreeDesktop Base Directory Specification. They should not actually be hard-coded but instead use the environment variables (i.e. $XDG_DATA_HOME, $XDG_CACHE_HOME, and $XDG_CONFIG_HOME). There are GLib and Python wrappers for the spec that may be helpful as well. Here's an example in Python:

>>> import xdg.BaseDirectory
>>> print xdg.BaseDirectory.xdg_data_home
/home/andrew/.local/share
>>> print xdg.BaseDirectory.xdg_config_home
/home/andrew/.config
>>> print xdg.BaseDirectory.xdg_cache_home
/home/andrew/.cache

.gnome and .gnome2 are indeed deprecated and should not be used. These were used by libgnome's gnome-config module.

.gconf does indeed contain the settings that gconf-editor accesses as xml files. For instance, compare the output of the following commands:

gconftool -a /desktop/gnome/applications/browser

cat ~/.gconf/desktop/gnome/applications/browser/%gconf.xml

As far as I know there is no issues with naming folders and files with a single or multiple dots.

Ubuntu generally does not use the dot and three characters (such as .txt) to identify the file type. So this has no special meaning in the Ubuntu context. This is useful when sharing files with Windows. Ubuntu uses Magic Numbers in the first few bytes of the file to identify the file type. However, Nautilus. ignores the magic numbers if the dot and three characters extension is available to identify the file type. This setting can be changed. See Force nautilus to ignore extensions

In Ubuntu, starting a file or folder names with a dot, such as .experiment_L0.5, makes the file or folder hidden. You can toggle the display of hidden files by pressing Ctrl+H in Nautilus. In Windows a file name starting with a . is not hidden. So if you transfer a hidden file named .experiment_L0.5 into a Windows system it will be plainly visible.

In Ubuntu a file name can end with a dot as it has no special meaning placed at the end. However, in Windows a dot separates the file name and extension, and a file name ending with a dot but no extension is not allowed. When I tried to create such a file in Windows I got a file with just the name, no dot, no extension.

Reference: Wiki on Filenames

Hope this helps.