Tree 2.0 and later will unconditionally ignore all options and write
JSON data on file descriptor 3 when available, which causes problems
for the test harness and other scripts that use FD 3.  Work around by
closing descriptor 3 for the 'tree' command.

POSIX sed doesn't support \+ in BREs which causes the regex that
extracts a file's current keys to return nothing, meaning that files
are unecessarily reencrypted.
This converts the regex in question to use ERE.

The `.extensions` directory can contain extensions code, for example as
git submodules, that have `.gpg` files as part of their code but that
are not files encrypted with the PGP keys of our password store.

One example is `pass-tomb`, that contains `.gpg` files in `tests/gnupg`,
but there are more, like `pass-update`, `pass-otp`, etc.

However those `.gpg` files in the `.extensions` directory are currently
processed by the `grep` and `reencrypt` functions of `pass`.

At best this can cause errors to be shown to the user when
grepping/reencrypting, and at worst it can cause files in the
`.extensions` directory to be decrypted and returned as part of a
search, or reencrypted with the incorrect PGP keys.

This patch tries to mitigate that issue by removing the `*/.extensions`
directories from the list of processed `.gpg` files for the
grep/reencrypt functions.

However this patch is not perfect as it does not take into account the
fact that the `.extensions` directory can be renamed to something else
using `PASSWORD_STORE_EXTENSIONS_DIR`. But knowing if this
`PASSWORD_STORE_EXTENSIONS_DIR` is inside the `PREFIX` or not and
formatting the path exclusion for `find` accordingly could require a
fair bit of additional logic that I am not sure how you want to
implement.

The 'which' command is an external command that must be called each and
every time pass is used. 'which' is also not mentioned in the README as
one of the dependencies that might be needed to run pass.

Instead of 'which', we can use the POSIX compatible and shell built-in
'command -v'. It saves pass from making an external call and is,
arguably, more reliable than using 'which' as mentioned in the following
link.

In the strange case that the user is jumping back and forth from X11 to
Wayland and viceversa, xclip might be installed but wl-clip might not,
and in such combination user might end up with the -c opion not working.

Afaik fish shell completions don't need a shebang
(plus the script is not executable anyway)

In MacOS Catalina, pass fails on accents with 'sed: RE error: illegal
byte sequence'.

I use a pass-specific gpg home directory. I tell pass about it by using
PASSWORD_STORE_GPG_OPTS="--homedir dir".
I also tell pass to sign files with PASSWORD_STORE_SIGNING_KEY.

However "pass init" returns "Signing of .gpg_id unsuccessful." because
we forgot to hand it GPG_OPTS. This patch fixes that oversight.