Here is the report.

name = 'pijul'
operating_system = 'unix:Arch'
crate_version = '1.0.0-alpha'
explanation = '''
Panic occurred in file '/home/lethom/.cargo/registry/src/github.com-1ecc6299db9ec823/libpijul-1.0.0-alpha/src/apply.rs' at line 89
'''
cause = 'assertion failed: workspace.is_empty()'
method = 'Panic'
backtrace = '''

   0: 0x56493999732e - pijul::commands::pushpull::Pull::run::{{closure}}::hcadd76a55d9d77dc
   1: 0x5649399ab548 - pijul::run::{{closure}}::hf654ae3fb02038aa
   2: 0x564939977002 - <core::future::from_generator::GenFuture<T> as core::future::future::Future>::poll::h2fafa0e8fc76e5cf
   3: 0x564939ad655f - tokio::runtime::enter::Enter::block_on::hb1938e178a0958d8
   4: 0x564939a1451b - tokio::runtime::thread_pool::ThreadPool::block_on::ha2e13a4da28ca949
   5: 0x5649399e0280 - tokio::runtime::context::enter::hfb24cf431904abb1
   6: 0x564939a995cc - tokio::runtime::handle::Handle::enter::h7d0c3648174b5925
   7: 0x564939a2f05d - pijul::main::hf4cca677e835d5d5
   8: 0x5649399d38b3 - std::sys_common::backtrace::__rust_begin_short_backtrace::hba130a261aead112
   9: 0x5649399d38c9 - std::rt::lang_start::{{closure}}::h2e734062e8c42398
  10: 0x56493a0af3c1 - core::ops::function::impls::<impl core::ops::function::FnOnce<A> for &F>::call_once::h6a3209f124be2235
                at /rustc/18bf6b4f01a6feaf7259ba7cdae58031af1b7b39/library/core/src/ops/function.rs:259
                 - std::panicking::try::do_call::h88ce358792b64df0
                at /rustc/18bf6b4f01a6feaf7259ba7cdae58031af1b7b39/library/std/src/panicking.rs:373
                 - std::panicking::try::h6311c259678e50fc
                at /rustc/18bf6b4f01a6feaf7259ba7cdae58031af1b7b39/library/std/src/panicking.rs:337
                 - std::panic::catch_unwind::h56c5716807d659a1
                at /rustc/18bf6b4f01a6feaf7259ba7cdae58031af1b7b39/library/std/src/panic.rs:379
                 - std::rt::lang_start_internal::h73711f37ecfcb277
                at /rustc/18bf6b4f01a6feaf7259ba7cdae58031af1b7b39/library/std/src/rt.rs:51
  11: 0x564939a2f162 - main
  12: 0x7f36a4ea8152 - __libc_start_main
  13: 0x56493990e2be - _start
  14:        0x0 - <unresolved>'''

It looks like this bug has been fixed in the latest pijul.

It has been fixed indeed, but thanks for reporting.