How is tea affecting water's color?
Where are they stored? (How does tea plant make them? I'm looking for the reactions that occur in the leaf)


Both citrate and oxalate are associated with ATP production via the citric acid cycle. As is obvious from the name, citrate is a critical component of the process. Oxalate is a hydrolysis product of oxaloacetic acid, which is also part of the cycle. Both of these ions are present within the plant cells.


  How and why do they get released from tea leaf? Since you don't usually see any "big" differences between tea leaf and a soaked tea leaf? (I'm not looking for the how of solution)


If your tea leaves are crushed or broken in any way, this really is just simple dissolution. If you have whole tea leaves, the oxalate and citrate are migrating into and out of the plant cells. The cell wall is permeable, so the ions (or corresponding acids) can simply flow through it. The cell membrane is semipermeable, and the diffusion of the ions across it is a biologically controlled process that I honestly don't have the background to explain.


  What makes the color of water change? Why does the color vary with pH alteration?


The pH and color are not related properties. The pH is affected by the citric acid and oxalic acid associated with the anions previously discussed, as well as other minor components that are likely present. The color comes from some of the many other compounds that are extracted into the water, which number in the hundreds, if not thousands. Some of these compounds are inherently colored - no reaction is required to produce color in the solution.