A marker file at the top of a Claude plugin folder hides the plugins under it
The same --plugin-dir flag, pointed at the same directory, produced two inventories. In the first, claude plugin list named alpha@inline at version 0.1.0 and beta@inline at version 0.1.0. Both rows said loaded. In the second, the same command named one row, plugins@inline, version unknown, and said that row was loaded too. Both commands exited 0. The child directories had not moved. Each still held a .claude-plugin/plugin.json and a skill file. The change between the two lists was a file at the top of the parent.