"What is the purpose of the directories inside .specify/ ?

[NestorJesusGuzman]

When I run /specify.specs it ends up creating a new specs directory instead of using the one inside the .specify/specs folder, and when I try to run /specify.plan and/or task I see that it generates the .md files inside the specs folder created in the first step.

So what are those folders that specify init creates for if they are not used?"

[mnriem]

The folders inside of the .specify directory are used to configure Spec Kit itself mostly

[wondr-wclabs]

The short version is: .specify/ is mostly Spec Kit’s project configuration and command infrastructure, while specs/ is where feature artifacts live.

In a normal initialized project:

• .specify/memory/constitution.md stores the project principles that guide later commands.
• .specify/templates/ stores the command/page templates Spec Kit uses.
• .specify/scripts/ stores helper scripts used by the generated commands.
• .specify/extensions/, .specify/presets/, and related config files are for customizing or extending how Spec Kit behaves.
• specs/<NNN-feature>/ is where feature output goes: spec.md, plan.md, tasks.md, and related artifacts.

So it is expected that /speckit.specify creates or uses a feature directory under specs/, not .specify/specs. The .specify tree is more like the local Spec Kit runtime/configuration for the project; the top-level specs/ tree is the product/specification history.

That split matters because upgrading or refreshing Spec Kit can touch .specify/scripts and .specify/templates, but your feature work in specs/ should remain separate from the tool’s own files.