Unless your lease says otherwise, air conditioners, lights, cabinets and shelves belong to the landlord. Tenants sometimes assume that if they paid for it, it's theirs. Even if your landlord has no use for the fixtures, she can keep the equipment and sell it. Either the general principles of law as described earlier, or your lease. In initial lease negotiations, improvements are more open to negotiation and hard bargaining than any other contract term.
Any construction costs over the allowance are the tenant's responsibility.
During the rental, other improvements may be added. Most commercial leases require a landlord's written permission for these. The tenant generally bears the full expense of later remodeling and additions. You'll probably be required to paint, plaster, re-floor, etc. You'll also have to pay for moving and re-installation at your new address.