Why do I need to type Ctrl-D twice to mark end-of-file?
On Unix-like systems (at least by default), an end-of-file condition is triggered by typing Ctrl-D at the beginning of a line or by typing Ctrl-D twice if you're not at the beginning of a line.
In the latter case, the last line you read will not have a '\n' at the end of it; you may need to allow for that.
This is specified (rather indirectly) by POSIX / The Open Group Base Specifications Issue 7, in section 11, specifically 11.1.9:
EOF
Special character on input, which is recognized if the ICANON flag is set. When received, all the bytes waiting to be read are immediately passed to the process without waiting for a <newline>, and the EOF is discarded. Thus, if there are no bytes waiting (that is, the EOF occurred at the beginning of a line), a byte count of zero shall be returned from the read(), representing an end-of-file indication. If ICANON is set, the EOF character shall be discarded when processed.
The POSIX read() function indicates an end-of-file (or error) condition to its caller by returning a byte count of zero, indicating that there are no more bytes of data to read. (C's <stdio> is, on POSIX systems, built on top of read() and other POSIX-specific functions.)
EOF (not to be confused with the C EOF macro) is mapped by default to Ctrl-D. Typing the EOF character at the beginning of a line (either at the very beginning of the input or immediately after a newline) triggers an immediate end-of-file condition. Typing the EOF character other than at the beginning of a line causes the previous data on that line to be returned immediately by the next read() call that asks for enough bytes; typing the EOF character again does the same thing, but in that case there are no remaining bytes to be read and an end-of-file condition is triggered. A single EOF character in the middle of a line is discarded (if ICANON is set, which it normally is).
In the off chance that someone sees this that needs the help I've been needing... I had been searching, trying to figure out why I was getting this strange behavior with my while(scanf). Well, it turns out that I had while (scanf("%s\n", string) > 0). The editor I am using (Atom) automatically put a "\n" in my scan, with out me noticing. This took me hours, and luckily someone pointed it out to me.