How do I increase my stamina?

The game has changed drastically since the last answer was posted:

• Running no longer uses Stamina. Only abilities consume stamina, in addition to heavy attacks.
• Running faster can be done by either:
  • Recombobulating melee weapons with the +#% movement speed" perk
  • Using the melee Six Feet Under which has a unique perk of "Hitting an enemy with this weapon grants +6% movement speed for 5 seconds. Stacks up to 5 times."
  • Entering Shadow Stance upon a melee kill as any Ninja
  • Using the Ninja Dire.
    • In the Commander slot he grants +50% movement speed at night
    • In the Support slot he grants +25% movement speed at night
  • Spending 2 BluGlo on a Movement Speed pylon

All heroes have some kind of bonus stat that is applied when they are in your hero squad. There are two kinds of bonus: a support bonus (left side hero), which gets applied no matter what, and a tactical bonus (right side), which only gets applied when the hero in the slot is star level 2 or higher.

There are some heroes that increase the amount of energy you have. I know Assassin Sarah has a 16% bonus to energy capacity as her support bonus. (This gives an extra 16 max energy.) Dim Mak increases the energy regeneration rate as a support bonus. There are probably some other heroes that also provide energy bonuses as well.