Typically, weapons are discrete, and a weapon just doesn’t and just can’t function as another weapon without the DM or the game having made some sort of exception, whether because of the weapon itself (whether through description or magical properties), because of the wielder’s special abilities (including feats and class features), or because of spells and the like.
A house rule allowing a halberd to function as a magic staff (which, by the way, the rules say must be at least a masterwork-on-one end quarterstaff), however, is unlikely to unbalance the game in any serious manner.
That said, to do this according to the rules anyway, the fighter/wizard/eldritch knight adds to his magic quarterstaff the following weapon special ability:
- The magic weapon special ability morphing (MIC 39) (+1 bonus; 0 lbs.) allows the wielder to take a standard action to transform a melee or thrown weapon into another weapon of the same size and effort. A typical weapon transformed into a double weapon applies its enhancement bonuses and weapon special abilities to one of the new weapon’s heads; a double weapon into a typical single weapon allows the wielder to pick which head’s enhancement bonus and weapon special abilities apply to the new weapon.
The transformation continues until the weapon’s transformed again, and magic quarterstaffs that are also magic staffs (and that’s totally a real thing) should function normally when transformed.1
There’s no precedent for a magic staff being anything but a magic staff
The vast amount of Dungeons and Dragons 3.5 material means I certainly may’ve missed something somewhere, but I know of no precedent for combining the feats Craft Magic Arms and Armor and Craft Staff to make a magic halberd that functions as a magic staff.
1 The 1st-level Sor/Wiz spell weapon shift (trans) (SpC 237) doesn’t work on quarterstaffs (or any other double weapon).