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The architectural reconfiguration system was a component of the Doctor's TARDIS in the shape of a tree that, according to the Eleventh Doctor, "reconstruct[ed] the particles according to your needs." It was basically "a machine that makes machines". It was, according to Gregor Van Baalen's scanner, "more valuable than the total sum of any currency."
In a timeline that was later erased, Gregor stole and disconnected one of the system's orbs out of pure greed, against the Doctor's warnings, and the TARDIS defended herself by locking him, Tricky and the Doctor in a space loop, as well as sealing the TARDIS doors. (TV: Journey to the Centre of the TARDIS)
Other TARDISes
During the Last Great Time War, Heleyna sabotaged Vassarian's Battle TARDIS reconfiguration system to stop the War Doctor from following her and stop her destruction of the Eye of Harmony. The Doctor used this idea and destroyed the Eye of Harmony chamber in this TARDIS to stop the Dalek Time Strategist's plan. (AUDIO: Eye of Harmony)
When the Twelfth Doctor trekked through a damaged TARDIS, he found it infested by Spyrillites, following them to the architectural reconfiguration system, the sight of it allowed him to realise that he was in TARDIS. (COMIC: Playing House)