What I suggest are some player-specific commands that can precisely alter the contents of a player's inventory with simple commands.
In the minecraft code, each inventory slot is addressed by a number, much like items and blocks have data values. the armor and crafting slots are also included in this count. some commands I suggest deal with directly altering a player's inventory and their ability to modify it.
/clear <player> - would very simply clear a player's inventory.
/equip <player> <item> <amount> <inv slot number> [data value] - would give a player the specific item and replace whatever they have in the aforementioned inv slot with the item specified.
/unnmovable <player> [item] - Disallows the player to move the specified item around their inventory, if none specified then no items are movable.
/undroppable <player> [item] [true/false] - Only disallows the removal of said item from the player inventory. If no item specified, then the player may not remove any items from his inventory. The true/false statement decides whether or not the player keeps the item upon death.
/take <player> <item/inv slot num> [amount] - will remove all of the stated item from the player's inv if no count specified, otherwise remove amount stated. If inv slot specified, then clear the specified inv slot, where if num specified then remove that number of items from said inv slot
/invblock <player> [item] - blocks the player from picking up the item specified/removing from GUI inventories (chests, dispensers), no items can be picked up if no item is declared.
/save <player> <name> - Saves the specified players inventory under a specific name.Will overwrite an inventory with the same name if it already exists.
/listinv - will list all available saved inventories by name.
/load <player> <name> - Replaces the specified player's inventory with the specified saved inventory.
/clearsave [name] - Clears all saved inventories. if name specified, then clears only that saved inventory. To prevent accidental loss, instead of deleting all inventories when a false name is presented, instead an error message should be displayed.
Just my ideas.
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"This is Blasphemy! This is madness!!"
"Madness... THIS IS MINECRAFT!!!!!"