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Let $G$ be a connected complex semi-simple Lie group and ${\mathcal{B}}$ its flag variety. For every positive integer $n$, we introduce a Poisson groupoid over ${\mathcal{B}}^n$, called the $n$th total configuration Poisson groupoid of flags of $G$, which contains a family of Poisson sub-groupoids whose total spaces are generalized double Bruhat cells and bases generalized Schubert cells. Certain symplectic leaves of these Poisson sub-groupoids are then shown to be symplectic groupoids over generalized Schubert cells. We also give explicit descriptions of symplectic leaves in three series of Poisson varieties associated to $G$.

Let $G$ be a connected and simply connected complex semisimple Lie group. For a collection of homogeneous $G$-spaces $G/Q$, we construct a finite atlas ${\mathcal{A}}_{\rm BS}(G/Q)$ on $G/Q$, called the Bott-Samelson atlas, and we prove that all of its coordinate functions are positive with respect to the Lusztig positive structure on $G/Q$. We also show that the standard Poisson structure $\pi_{G/Q}$ on $G/Q$ is presented, in each of the coordinate charts of ${\mathcal{A}}_{\rm BS}(G/Q)$, as a symmetric Poisson CGL extension (or a certain localization thereof) in the sense of Goodearl-Yakimov, making $(G/Q, \pi_{G/Q}, {\mathcal{A}}_{\rm BS}(G/Q))$ into a Poisson-Ore variety. Examples of $G/Q$ include $G$ itself, $G/T$, $G/B$, and $G/N$, where $T \subset G$ is a maximal torus, $B \subset G$ a Borel subgroup, and $N$ the uniradical of $B$.