changes files mode to more secure values, and updates the README.md about chmod

As said in issue #327, a 0777 file mode is a bad thing.
This commit changes permissions of all files with 0644 (and 0755 for folders).
The only one modified file is README.md.

I've edited the wiki for following good practices with exact commands to use.
Using this commit and following the wiki should not cause any problems, if the wiki instructions are followed.

Web hosting services which doesn't provides ssh access uses the same user for ftp access and web server, so permissions are already correct and there is nothing to do.