1. It does mean cluttered; dwarves will work more slowly in a cluttered workshop. The more cluttered it is, the more slowly they'll work.
2. They mean, respectively, that there are new sparring reports and new combat reports since the last time you entered the (r)eports screen. Sparring reports are, obviously, created by sparring dwarves, and combat reports are created by non-sparring, non-hunting combat. There's also the possibility of a green H that signifies new hunting reports, which, obviously, are created by combat due to a hunter hunting.
3. You let them become more skilled. When they get a skill up while they're active military and have (after the skill up) at least Great level in a weapon skill, they'll become a weapon lord. Note that, while they lose the Lord title after switching to civilian status, they do not lose any skill.
4. You can encrust items with cut gems, which increases the decorated item's value. Since cut gems don't have any quality modifier and decorations do, this increases your fort value.
5. You set the bed which is used to define the room to be a dormitory.
6. You arrange for your dwarves to dodge attacks, or have them watch dodging demonstrations. Combat and sparring will cause occasional dodges, as will a danger room (which is technically combat), which involves setting training spears in upright spike traps, setting them to trigger repeatedly, and letting your prospective soldiers stand around on them and get poked a lot. Note that danger rooms are actually dangerous if your dwarves don't have armor, so make sure that at least the torso and head are covered on any danger-room trained dwarves.