Pylint running from wrong directory [Import Error]

## Information

**VIM version**

VIM - Vi IMproved 8.0 (2016 Sep 12, compiled Mar 18 2020 18:29:15)
Included patches: 1-1453

Operating System:
Linux nginsburg-desktop 4.15.0-91-generic #92-Ubuntu SMP Fri Feb 28 11:09:48 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux

## What went wrong

As I filled out this bug report I kinda figured out what's wrong

Project structure
```
gitrepo/
/main_file
/{bunch of project metadata files}
/lib
/__init__.py
/{a few module folders}
/plugins <- this directory is in my git ignore
/__init__.py
/{a few git repos here} <- these directories are completely separate repos
```
Opening a file in the `plugins` directory results in an import error in ALE.
Running pylint directly against that file does not result in any errors reported
Opening a file with ALE disabled, and using syntastic instead results in no errors reported
So there's some logical difference between the syntastic pylint linter and the ale pylint linter.

Opening a file outside of the `plugins` directory works as expected

I'm not good at vim scripts, so I'm not really sure exactly what's happening here or how to reasonably debug it. But it feels like pylint is being called from the wrong directory.

So I tried setting `let g:ale_python_pylint_change_directory = 1` explicitly but there was no difference (which I guess is expected)

I then set it to `0` and it no longer reports the import error, what appears to be happening is that the pylint change directory is assuming the incorrect project root.

I think this is actually a bug because in your help

> this is necessary for `pylint` to use a project `pylintrc` file, if present.

This suggests ale cannot utilize the projects pylintrc file.

Also, both pylint and syntastic are able to determine the correct output for these files.

Are you having trouble configuring ALE? Try asking for help on [Stack Exchange](https://vi.stackexchange.com/) or perhaps on [Reddit](https://www.reddit.com/r/vim/) instead. The GitHub issue tracker should be used for reporting bugs or asking for new features.

## Reproducing the bug

1. I embeded git repos
2. Then got misreported pylint errors

### :ALEInfo
Called `vim libcopacetic/plugins/fleet/models/__init__.py`
from vim called `ALEInfo`
Got this: From the output it does look like Ale is calling pylint from the wrong directory.

```
Current Filetype: python
Available Linters: ['bandit', 'flake8', 'mypy', 'prospector', 'pycodestyle', 'pydocstyle', 'pyflakes', 'pyl
ama', 'pylint', 'pyls', 'pyre', 'vulture']
Enabled Linters: ['pylint']
Suggested Fixers:
'add_blank_lines_for_python_control_statements' - Add blank lines before control statements.
'autopep8' - Fix PEP8 issues with autopep8.
'black' - Fix PEP8 issues with black.
'isort' - Sort Python imports with isort.
'remove_trailing_lines' - Remove all blank lines at the end of a file.
'reorder-python-imports' - Sort Python imports with reorder-python-imports.
'trim_whitespace' - Remove all trailing whitespace characters at the end of every line.
'yapf' - Fix Python files with yapf.
Linter Variables:
let g:ale_python_auto_pipenv = 0
let g:ale_python_pylint_auto_pipenv = 0
let g:ale_python_pylint_change_directory = 1
let g:ale_python_pylint_executable = 'pylint'
let g:ale_python_pylint_options = ''
let g:ale_python_pylint_use_global = 0
let g:ale_python_pylint_use_msg_id = 0
Global Variables:
let g:ale_cache_executable_check_failures = v:null
let g:ale_change_sign_column_color = 0
let g:ale_command_wrapper = ''
let g:ale_completion_delay = v:null
let g:ale_completion_enabled = 0
let g:ale_completion_max_suggestions = v:null
let g:ale_echo_cursor = 1
let g:ale_echo_msg_error_str = 'Error'
let g:ale_echo_msg_format = '%code: %%s'
let g:ale_echo_msg_info_str = 'Info'
let g:ale_echo_msg_warning_str = 'Warning'
let g:ale_enabled = 1
let g:ale_fix_on_save = 0
let g:ale_fixers = {}
let g:ale_history_enabled = 1
let g:ale_history_log_output = 1
let g:ale_keep_list_window_open = 0
let g:ale_lint_delay = 200
let g:ale_lint_on_enter = 1
let g:ale_lint_on_filetype_changed = 1
let g:ale_lint_on_insert_leave = 1
let g:ale_lint_on_save = 1
let g:ale_lint_on_text_changed = 'normal'
let g:ale_linter_aliases = {}
let g:ale_linters = {'vim': ['vint'], 'go': ['golint'], 'puppet': ['puppet-lint'], 'json': ['jq'], 'ansible
': ['ansible-lint'], 'yaml': ['yamllint'], 'bash': ['shellcheck'], 'python': ['pylint']}
let g:ale_linters_explicit = 0
let g:ale_list_vertical = 0
let g:ale_list_window_size = 10
let g:ale_loclist_msg_format = '%code: %%s'
let g:ale_lsp_root = {}
let g:ale_max_buffer_history_size = 20
let g:ale_max_signs = -1
let g:ale_maximum_file_size = v:null
let g:ale_open_list = 1
let g:ale_pattern_options = v:null
let g:ale_pattern_options_enabled = v:null
let g:ale_set_balloons = 0
let g:ale_set_highlights = 1
let g:ale_set_loclist = 1
let g:ale_set_quickfix = 0
let g:ale_set_signs = 1
let g:ale_sign_column_always = 0
let g:ale_sign_error = '>>'
let g:ale_sign_info = '--'
let g:ale_sign_offset = 1000000
let g:ale_sign_style_error = '>>'
let g:ale_sign_style_warning = '--'
let g:ale_sign_warning = '--'
let g:ale_sign_highlight_linenrs = 0
let g:ale_statusline_format = v:null
let g:ale_type_map = {}
let g:ale_use_global_executables = v:null
let g:ale_virtualtext_cursor = 0
let g:ale_warn_about_trailing_blank_lines = 1
let g:ale_warn_about_trailing_whitespace = 1
Command History:
(executable check - success) /home/n0g/git/copacetic/venv/bin/pylint
(finished - exit code 2) ['/bin/bash', '-c', 'cd ''/home/n0g/git/copacetic/libcopacetic/plugins/fleet'' && ''/home/n0g/git/copacetic/venv/bin/pylint'' --output-format text --msg-template="{path}:{line}:{column}:
{msg_id} ({symbol}) {msg}" --reports n ''/home/n0g/git/copacetic/libcopacetic/plugins/fleet/models/__init__.py''']
<<>>
************* Module models
models/__init__.py:1:0: E0401 (import-error) Unable to import 'models.host'
models/__init__.py:2:0: E0401 (import-error) Unable to import 'models.interface'
----------------------------------------------------------------------
Your code has been rated at -40.00/10 (previous run: -40.00/10, +0.00)
<<>>
```