fix(fs): allow open, seek and fstat in the write permission sets (#3630)

* fix(fs): allow open, seek and fstat in the write permission sets

The stream path of writeFile calls `open`, which only the nested command
list of `allow-write-file` granted (plugins/fs/permissions/write-all.toml,
write-files.toml), so `fs:allow-appdata-write-recursive` and the other
write sets rejected streamed writes; seek/fstat were missing for
FileHandles created under these sets.

Adds open, seek and fstat to write-all and write-files. This widens the
write sets slightly (open is already implied by allow-write-file); the
generated reference does not list set members, so nothing to regenerate.

* use dependencies instead

plugins/fs/permissions/write-all.toml

@@ -1,17 +1,17 @@
 "$schema" = "schemas/schema.json"
 
-[[permission]]
+[[set]]
 identifier = "write-all"
 description = "This enables all write related commands without any pre-configured accessible paths."
-commands.allow = [
-  "mkdir",
-  "create",
-  "copy_file",
-  "remove",
-  "rename",
-  "truncate",
-  "ftruncate",
-  "write",
-  "write_file",
-  "write_text_file",
+permissions = [
+  "allow-mkdir",
+  "allow-create",
+  "allow-copy-file",
+  "allow-remove",
+  "allow-rename",
+  "allow-truncate",
+  "allow-ftruncate",
+  "allow-write",
+  "allow-write-file",
+  "allow-write-text-file",
 ]