A few of the extra and alternative sounds and effects a composer can ask of from the flautist.
Different ways of fingering notes. A verbal instruction in the music and a fingering diagram. There is no need to specify fingerings normally, so the use of alternative fingerings is generally left to the player. Occasionally a composer will require a specific alternative fingering because of its timbral characteristics.
South American-style sound. Normal notation, but with verbal instruction. The end barrel is pulled out and the mouthpiece turned inwards towards the player. An interesting effect, but with little carrying power.
Intervals smaller than a semitone. Notation methods vary, but these examples are typical of quartertones and raised & lowered inflections. Microtones are especially difficult on the piccolo, where the holes are entirely covered by keys. They are mostly produced using lip inflection.
Playing chords - more than one note at a time. Write the bottom note of the chord and the word 'chord' above. Occasionally composers write all the notes of the chord that they wish to hear and/or provide a fingering diagram.
Slapping instrument keys. X-shaped noteheads and verbal instruction. The larger the flute, the more effective and pitched the key slap.
Blowing a very small amount of air into the flute. Verbal instruction in the music. Although this is a quiet and somewhat uncontrollable effect, it has more carrying power than one might suppose.