"End Run" means a deviation from some standard, settled means, procedure, practice, or norm. There is an implication of surreptitious behavior. The phrase is derived from the American football offensive "trick play" in which a team typically fakes a sweep with nearly all players to one side of the field but hands the ball off to the end (typically lined up well away from the main group of players) who heads across field in exactly the opposite direction of the flow. Generally the defense does not expect the end to get the ball and will not be watching him in this type of scenario. It will often work at most once a game, because once the defense is burnt on the play, they are watching for it.
Jane did not attend the board meeting for the proposed city housing project, nor did she submit papers for the project. Instead, she ran an end run as she simply found five guys to start building the housing project and paid for the work out of the milk fund. This was legal as it took advantage of an obscure line in a 50,000 page rule book nobody was aware of. After this, the city council became wary and passed a new law regarding housing starts -- they need council approval.