refactor(init): call init_repo_dirs to create canonical layout
muse init was creating dirs inline via _INIT_SUBDIRS, missing remotes/, logs/, and shelf/ that init_repo_dirs defines as canonical. Now calls init_repo_dirs(cwd) first, then layers any init-specific extras (tags/, cache/) on top. Idempotent — existing repos are unaffected.
sha256:3adc80868d1bdefb27121d26dc5ec7aad486467dc900c0856d05231aa37c848b
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sha256:d09ca8a3169edbdc5310fabfe192e0d4f30f146c2802d3c6e12778c91c9a24b1
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