Battery doctor is bs app. Apple has designed the phone to draw the proper current depending on the charge state of the battery. At 99% it goes into trickle charge, which takes it to 100% and shuts of. It will cycle on and off trickle charging showing 99-100%. This is designed to not harm the battery.
In fact the whole charging regime engineered into the iPhone, takes into account not allowing Li Ion battery to either go under voltage to the damage point, or over charge to damage point. You can use the 5 watt cube that came with the phone or the 12 watt iPad charger. Both are approved, and will not harm the phone.
If you let the phone drain completely to where it shuts off. It is still above any damage point. However if you leave phone this way for months, voltage could drop to damage levels and battery might not take a charge with normal charger. Long term storage is best done at around 60-70 percent.
About only thing that will damage Li Ion batteries is excessive heat, or cold. If an app hangs up and the radios are beaming at high levels, processor cycling at max, phone sits on dashboard of car in sun, those are things that will damage battery.
Realize that when you manufacture millions of devices, their will be defective ones that slip through quality control. So if you have an overheating phone, or one that cannot take a charge, go to Apple Store and have them check it out. We are not dealing with Samsung here, you have a place that will check phone and replace/fix if needed.
Here is what I am seeing for a charge from my 6s Plus, with which I am quite satisfied with.
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