improve directory deletion/editing handling

passKitTests/Fixtures/password-store-empty-dirs.git/HEAD

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+ref: refs/heads/main

passKitTests/Fixtures/password-store-empty-dirs.git/config

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+[core]
+	repositoryformatversion = 0
+	filemode = true
+	bare = true
+	ignorecase = true
+	precomposeunicode = true

passKitTests/Fixtures/password-store-empty-dirs.git/description

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+Unnamed repository; edit this file 'description' to name the repository.

passKitTests/Fixtures/password-store-empty-dirs.git/info/exclude

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+# git ls-files --others --exclude-from=.git/info/exclude
+# Lines that start with '#' are comments.
+# For a project mostly in C, the following would be a good set of
+# exclude patterns (uncomment them if you want to use them):
+# *.[oa]
+# *~

passKitTests/Fixtures/password-store-empty-dirs.git/packed-refs

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+# pack-refs with: peeled fully-peeled sorted 
+fbcbb5819e1c864ef33cfffa179a71387a5d90d0 refs/heads/main