Meaning
The whole thing.

Origin

I've seen it suggested that this phrase refers to all of a shopkeeper's possessions - the stock in trade, the items stored in barrels and the lock to the door. This explanation is entirely fanciful though - the 'whole thing' in question when this phrase originated was a musket. Muskets were composed of three parts:

• The lock, or flintlock, which is the firing mechanism. Various forms of 'lock' muskets were used from the 1400s onwards, e.g. firelocks, flintlocks, matchlocks etc. The term 'lock' was probably adopted because the mechanism resembles a door lock.
  
• The stock, which is the wooden butt-end of the gun. 'Stock' is the old term for wooden butt or stump and is a generic term for a solid base. It was used as early as 1495 in association with Tudor guns, in a bill for 'gonne stokkes'. See also laughing stock.
  
• The barrel, i.e. a cylindrical object, is an even older word and was well-established by the 15th century. This is the least obvious of these three terms to have been chosen to name a musket part. After all, in the 15th century people would have been very familiar with barrels as the squat coopered tubs used for storage - hardly similar to the parallel-sided cylindrical tubes that were used in muskets. It may have been that the term migrated from cannons or other sorts of gun which were more barrel-shaped.

Note: that 'lock, stock and barrel' refers to muskets, not rifles. What makes rifles different from earlier guns are the spiral grooves inside the barrel, which cause the bullet to rotate and fly more truly. 'Rifle' derives from the French verb 'rifler' - to scratch or scrape.

From: http://www.phrases.org.uk/