diff --git a/ale_linters/ada/gcc.vim b/ale_linters/ada/gcc.vim
index d6f973ae..7b0c4809 100644
--- a/ale_linters/ada/gcc.vim
+++ b/ale_linters/ada/gcc.vim
@@ -12,7 +12,7 @@ function! ale_linters#ada#gcc#GetCommand(buffer) abort
     " the .ali file may be created even if no code generation is attempted.
     " The output file name must match the source file name (except for the
     " extension), so here we cannot use the null file as output.
-    let l:tmp_dir = fnamemodify(ale#engine#CreateDirectory(a:buffer), ':p')
+    let l:tmp_dir = fnamemodify(ale#command#CreateDirectory(a:buffer), ':p')
     let l:out_file = l:tmp_dir . fnamemodify(bufname(a:buffer), ':t:r') . '.o'
 
     " -gnatc: Check syntax and semantics only (no code generation attempted)
diff --git a/ale_linters/cs/mcsc.vim b/ale_linters/cs/mcsc.vim
index 1561661e..a169297c 100644
--- a/ale_linters/cs/mcsc.vim
+++ b/ale_linters/cs/mcsc.vim
@@ -30,7 +30,7 @@ function! ale_linters#cs#mcsc#GetCommand(buffer) abort
 
     " register temporary module target file with ale
     " register temporary module target file with ALE.
-    let l:out = ale#engine#CreateFile(a:buffer)
+    let l:out = ale#command#CreateFile(a:buffer)
 
     " The code is compiled as a module and the output is redirected to a
     " temporary file.
diff --git a/ale_linters/cuda/nvcc.vim b/ale_linters/cuda/nvcc.vim
index f4442cb8..db789ff1 100644
--- a/ale_linters/cuda/nvcc.vim
+++ b/ale_linters/cuda/nvcc.vim
@@ -7,7 +7,7 @@ call ale#Set('cuda_nvcc_options', '-std=c++11')
 function! ale_linters#cuda#nvcc#GetCommand(buffer) abort
     " Unused: use ale#util#nul_file
     " let l:output_file = ale#util#Tempname() . '.ii'
-    " call ale#engine#ManageFile(a:buffer, l:output_file)
+    " call ale#command#ManageFile(a:buffer, l:output_file)
     return '%e -cuda'
     \   . ale#Pad(ale#c#IncludeOptions(ale#c#FindLocalHeaderPaths(a:buffer)))
     \   . ale#Pad(ale#Var(a:buffer, 'cuda_nvcc_options'))
diff --git a/ale_linters/elixir/mix.vim b/ale_linters/elixir/mix.vim
index dc3c1818..59cfe505 100644
--- a/ale_linters/elixir/mix.vim
+++ b/ale_linters/elixir/mix.vim
@@ -32,7 +32,7 @@ endfunction
 function! ale_linters#elixir#mix#GetCommand(buffer) abort
     let l:project_root = ale#handlers#elixir#FindMixProjectRoot(a:buffer)
 
-    let l:temp_dir = ale#engine#CreateDirectory(a:buffer)
+    let l:temp_dir = ale#command#CreateDirectory(a:buffer)
 
     let l:mix_build_path = has('win32')
     \   ? 'set MIX_BUILD_PATH=' . ale#Escape(l:temp_dir) . ' &&'
diff --git a/ale_linters/erlang/erlc.vim b/ale_linters/erlang/erlc.vim
index 0bdb4dea..81ba128b 100644
--- a/ale_linters/erlang/erlc.vim
+++ b/ale_linters/erlang/erlc.vim
@@ -4,7 +4,7 @@ let g:ale_erlang_erlc_options = get(g:, 'ale_erlang_erlc_options', '')
 
 function! ale_linters#erlang#erlc#GetCommand(buffer) abort
     let l:output_file = ale#util#Tempname()
-    call ale#engine#ManageFile(a:buffer, l:output_file)
+    call ale#command#ManageFile(a:buffer, l:output_file)
 
     return 'erlc -o ' . ale#Escape(l:output_file)
     \   . ' ' . ale#Var(a:buffer, 'erlang_erlc_options')
diff --git a/ale_linters/java/javac.vim b/ale_linters/java/javac.vim
index 63dcdd94..2aa01b4f 100644
--- a/ale_linters/java/javac.vim
+++ b/ale_linters/java/javac.vim
@@ -73,7 +73,7 @@ function! ale_linters#java#javac#GetCommand(buffer, import_paths) abort
     endif
 
     " Create .class files in a temporary directory, which we will delete later.
-    let l:class_file_directory = ale#engine#CreateDirectory(a:buffer)
+    let l:class_file_directory = ale#command#CreateDirectory(a:buffer)
 
     " Always run javac from the directory the file is in, so we can resolve
     " relative paths correctly.
diff --git a/ale_linters/thrift/thrift.vim b/ale_linters/thrift/thrift.vim
index 36a8656e..2f2086c9 100644
--- a/ale_linters/thrift/thrift.vim
+++ b/ale_linters/thrift/thrift.vim
@@ -16,7 +16,7 @@ function! ale_linters#thrift#thrift#GetCommand(buffer) abort
         let l:generators = ['cpp']
     endif
 
-    let l:output_dir = ale#engine#CreateDirectory(a:buffer)
+    let l:output_dir = ale#command#CreateDirectory(a:buffer)
 
     return '%e'
     \   . ale#Pad(join(map(copy(l:generators), "'--gen ' . v:val")))
diff --git a/ale_linters/verilog/verilator.vim b/ale_linters/verilog/verilator.vim
index 83d5f59d..18d99043 100644
--- a/ale_linters/verilog/verilator.vim
+++ b/ale_linters/verilog/verilator.vim
@@ -10,7 +10,7 @@ function! ale_linters#verilog#verilator#GetCommand(buffer) abort
     let l:filename = ale#util#Tempname() . '_verilator_linted.v'
 
     " Create a special filename, so we can detect it in the handler.
-    call ale#engine#ManageFile(a:buffer, l:filename)
+    call ale#command#ManageFile(a:buffer, l:filename)
     let l:lines = getbufline(a:buffer, 1, '$')
     call ale#util#Writefile(a:buffer, l:lines, l:filename)
 
diff --git a/ale_linters/vim/ale_custom_linting_rules.vim b/ale_linters/vim/ale_custom_linting_rules.vim
index 3da44206..3abe5d4b 100644
--- a/ale_linters/vim/ale_custom_linting_rules.vim
+++ b/ale_linters/vim/ale_custom_linting_rules.vim
@@ -25,7 +25,7 @@ endfunction
 function! ale_linters#vim#ale_custom_linting_rules#GetCommand(buffer) abort
     let l:dir = s:GetALEProjectDir(a:buffer)
 
-    let l:temp_dir = ale#engine#CreateDirectory(a:buffer)
+    let l:temp_dir = ale#command#CreateDirectory(a:buffer)
     let l:temp_file = l:temp_dir . '/example.vim'
 
     let l:lines = getbufline(a:buffer, 1, '$')
diff --git a/autoload/ale/command.vim b/autoload/ale/command.vim
index 6c56d518..6944f170 100644
--- a/autoload/ale/command.vim
+++ b/autoload/ale/command.vim
@@ -1,6 +1,121 @@
 " Author: w0rp <devw0rp@gmail.com>
-" Description: Special command formatting for creating temporary files and
-" passing buffer filenames easily.
+" Description: Functions for formatting command strings, running commands, and
+"   managing files during linting and fixing cycles.
+
+" This dictionary holds lists of files and directories to remove later.
+if !exists('s:managed_data')
+    let s:managed_data = {}
+endif
+
+" Used to get the data in tests.
+function! ale#command#GetData() abort
+    return deepcopy(s:managed_data)
+endfunction
+
+function! ale#command#ClearData() abort
+    let s:managed_data = {}
+endfunction
+
+function! ale#command#ManageFile(buffer, file) abort
+    if !has_key(s:managed_data, a:buffer)
+        let s:managed_data[a:buffer] = {'file_list': [], 'directory_list': []}
+    endif
+
+    call add(s:managed_data[a:buffer].file_list, a:file)
+endfunction
+
+function! ale#command#ManageDirectory(buffer, directory) abort
+    if !has_key(s:managed_data, a:buffer)
+        let s:managed_data[a:buffer] = {'file_list': [], 'directory_list': []}
+    endif
+
+    call add(s:managed_data[a:buffer].directory_list, a:directory)
+endfunction
+
+function! ale#command#CreateFile(buffer) abort
+    " This variable can be set to 1 in tests to stub this out.
+    if get(g:, 'ale_create_dummy_temporary_file')
+        return 'TEMP'
+    endif
+
+    let l:temporary_file = ale#util#Tempname()
+    call ale#command#ManageFile(a:buffer, l:temporary_file)
+
+    return l:temporary_file
+endfunction
+
+" Create a new temporary directory and manage it in one go.
+function! ale#command#CreateDirectory(buffer) abort
+    " This variable can be set to 1 in tests to stub this out.
+    if get(g:, 'ale_create_dummy_temporary_file')
+        return 'TEMP_DIR'
+    endif
+
+    let l:temporary_directory = ale#util#Tempname()
+    " Create the temporary directory for the file, unreadable by 'other'
+    " users.
+    call mkdir(l:temporary_directory, '', 0750)
+    call ale#command#ManageDirectory(a:buffer, l:temporary_directory)
+
+    return l:temporary_directory
+endfunction
+
+function! ale#command#RemoveManagedFiles(buffer) abort
+    let l:info = get(s:managed_data, a:buffer, {})
+
+    if !empty(l:info)
+    \&& (
+    \   !exists('*ale#engine#IsCheckingBuffer')
+    \   || !ale#engine#IsCheckingBuffer(a:buffer)
+    \)
+    \&& (
+    \   !has_key(g:ale_fix_buffer_data, a:buffer)
+    \   || g:ale_fix_buffer_data[a:buffer].done
+    \)
+        " We can't delete anything in a sandbox, so wait until we escape from
+        " it to delete temporary files and directories.
+        if ale#util#InSandbox()
+            return
+        endif
+
+        " Delete files with a call akin to a plan `rm` command.
+        for l:filename in l:info.file_list
+            call delete(l:filename)
+        endfor
+
+        " Delete directories like `rm -rf`.
+        " Directories are handled differently from files, so paths that are
+        " intended to be single files can be set up for automatic deletion
+        " without accidentally deleting entire directories.
+        for l:directory in l:info.directory_list
+            call delete(l:directory, 'rf')
+        endfor
+
+        call remove(s:managed_data, a:buffer)
+    endif
+endfunction
+
+function! ale#command#CreateTempFile(buffer, temporary_file, input) abort
+    if empty(a:temporary_file)
+        " There is no file, so we didn't create anything.
+        return 0
+    endif
+
+    " Use an existing list of lines of input if we have it, or get the lines
+    " from the file.
+    let l:lines = a:input isnot v:null ? a:input : getbufline(a:buffer, 1, '$')
+
+    let l:temporary_directory = fnamemodify(a:temporary_file, ':h')
+    " Create the temporary directory for the file, unreadable by 'other'
+    " users.
+    call mkdir(l:temporary_directory, '', 0750)
+    " Automatically delete the directory later.
+    call ale#command#ManageDirectory(a:buffer, l:temporary_directory)
+    " Write the buffer out to a file.
+    call ale#util#Writefile(a:buffer, l:lines, a:temporary_file)
+
+    return 1
+endfunction
 
 function! s:TemporaryFilename(buffer) abort
     let l:filename = fnamemodify(bufname(a:buffer), ':t')
@@ -16,11 +131,17 @@ function! s:TemporaryFilename(buffer) abort
     return ale#util#Tempname() . (has('win32') ? '\' : '/') . l:filename
 endfunction
 
+" Given part of a command, replace any % with %%, so that no characters in
+" the string will be replaced with filenames, etc.
+function! ale#command#EscapeCommandPart(command_part) abort
+    return substitute(a:command_part, '%', '%%', 'g')
+endfunction
+
 " Given a command string, replace every...
 " %s -> with the current filename
 " %t -> with the name of an unused file in a temporary directory
 " %% -> with a literal %
-function! ale#command#FormatCommand(buffer, executable, command, pipe_file_if_needed, CreateTemporaryFileForJob) abort
+function! ale#command#FormatCommand(buffer, executable, command, pipe_file_if_needed, input) abort
     let l:temporary_file = ''
     let l:command = a:command
 
@@ -40,7 +161,7 @@ function! ale#command#FormatCommand(buffer, executable, command, pipe_file_if_ne
         let l:command = substitute(l:command, '%s', '\=ale#Escape(l:filename)', 'g')
     endif
 
-    if l:command =~# '%t'
+    if a:input isnot v:false && l:command =~# '%t'
         " Create a temporary filename, <temp_dir>/<original_basename>
         " The file itself will not be created by this function.
         let l:temporary_file = s:TemporaryFilename(a:buffer)
@@ -58,7 +179,11 @@ function! ale#command#FormatCommand(buffer, executable, command, pipe_file_if_ne
         let l:command = l:command . ' < ' . ale#Escape(l:temporary_file)
     endif
 
-    let l:file_created = a:CreateTemporaryFileForJob(a:buffer, l:temporary_file)
+    let l:file_created = ale#command#CreateTempFile(
+    \   a:buffer,
+    \   l:temporary_file,
+    \   a:input,
+    \)
 
     return [l:temporary_file, l:command, l:file_created]
 endfunction
diff --git a/autoload/ale/engine.vim b/autoload/ale/engine.vim
index ace123dc..c3313512 100644
--- a/autoload/ale/engine.vim
+++ b/autoload/ale/engine.vim
@@ -74,15 +74,11 @@ function! ale#engine#InitBufferInfo(buffer) abort
         " job_list will hold the list of job IDs
         " active_linter_list will hold the list of active linter names
         " loclist holds the loclist items after all jobs have completed.
-        " temporary_file_list holds temporary files to be cleaned up
-        " temporary_directory_list holds temporary directories to be cleaned up
         let g:ale_buffer_info[a:buffer] = {
         \   'job_list': [],
         \   'active_linter_list': [],
         \   'active_other_sources_list': [],
         \   'loclist': [],
-        \   'temporary_file_list': [],
-        \   'temporary_directory_list': [],
         \}
 
         return 1
@@ -104,73 +100,25 @@ endfunction
 " Register a temporary file to be managed with the ALE engine for
 " a current job run.
 function! ale#engine#ManageFile(buffer, filename) abort
-    call ale#engine#InitBufferInfo(a:buffer)
-    call add(g:ale_buffer_info[a:buffer].temporary_file_list, a:filename)
+    " TODO: Emit deprecation warning here later.
+    call ale#command#ManageFile(a:buffer, a:filename)
 endfunction
 
 " Same as the above, but manage an entire directory.
 function! ale#engine#ManageDirectory(buffer, directory) abort
-    call ale#engine#InitBufferInfo(a:buffer)
-    call add(g:ale_buffer_info[a:buffer].temporary_directory_list, a:directory)
+    " TODO: Emit deprecation warning here later.
+    call ale#command#ManageDirectory(a:buffer, a:directory)
 endfunction
 
 function! ale#engine#CreateFile(buffer) abort
-    " This variable can be set to 1 in tests to stub this out.
-    if get(g:, 'ale_create_dummy_temporary_file')
-        return 'TEMP'
-    endif
-
-    let l:temporary_file = ale#util#Tempname()
-    call ale#engine#ManageFile(a:buffer, l:temporary_file)
-
-    return l:temporary_file
+    " TODO: Emit deprecation warning here later.
+    return ale#command#CreateFile(a:buffer)
 endfunction
 
 " Create a new temporary directory and manage it in one go.
 function! ale#engine#CreateDirectory(buffer) abort
-    " This variable can be set to 1 in tests to stub this out.
-    if get(g:, 'ale_create_dummy_temporary_file')
-        return 'TEMP_DIR'
-    endif
-
-    let l:temporary_directory = ale#util#Tempname()
-    " Create the temporary directory for the file, unreadable by 'other'
-    " users.
-    call mkdir(l:temporary_directory, '', 0750)
-    call ale#engine#ManageDirectory(a:buffer, l:temporary_directory)
-
-    return l:temporary_directory
-endfunction
-
-function! ale#engine#RemoveManagedFiles(buffer) abort
-    let l:info = get(g:ale_buffer_info, a:buffer, {})
-
-    " We can't delete anything in a sandbox, so wait until we escape from
-    " it to delete temporary files and directories.
-    if ale#util#InSandbox()
-        return
-    endif
-
-    " Delete files with a call akin to a plan `rm` command.
-    if has_key(l:info, 'temporary_file_list')
-        for l:filename in l:info.temporary_file_list
-            call delete(l:filename)
-        endfor
-
-        let l:info.temporary_file_list = []
-    endif
-
-    " Delete directories like `rm -rf`.
-    " Directories are handled differently from files, so paths that are
-    " intended to be single files can be set up for automatic deletion without
-    " accidentally deleting entire directories.
-    if has_key(l:info, 'temporary_directory_list')
-        for l:directory in l:info.temporary_directory_list
-            call delete(l:directory, 'rf')
-        endfor
-
-        let l:info.temporary_directory_list = []
-    endif
+    " TODO: Emit deprecation warning here later.
+    return ale#command#CreateDirectory(a:buffer)
 endfunction
 
 function! s:GatherOutput(job_id, line) abort
@@ -321,7 +269,7 @@ function! ale#engine#SetResults(buffer, loclist) abort
 
         " Automatically remove all managed temporary files and directories
         " now that all jobs have completed.
-        call ale#engine#RemoveManagedFiles(a:buffer)
+        call ale#command#RemoveManagedFiles(a:buffer)
 
         " Call user autocommands. This allows users to hook into ALE's lint cycle.
         silent doautocmd <nomodeline> User ALELintPost
@@ -472,26 +420,8 @@ endfunction
 " Given part of a command, replace any % with %%, so that no characters in
 " the string will be replaced with filenames, etc.
 function! ale#engine#EscapeCommandPart(command_part) abort
-    return substitute(a:command_part, '%', '%%', 'g')
-endfunction
-
-function! s:CreateTemporaryFileForJob(buffer, temporary_file) abort
-    if empty(a:temporary_file)
-        " There is no file, so we didn't create anything.
-        return 0
-    endif
-
-    let l:temporary_directory = fnamemodify(a:temporary_file, ':h')
-    " Create the temporary directory for the file, unreadable by 'other'
-    " users.
-    call mkdir(l:temporary_directory, '', 0750)
-    " Automatically delete the directory later.
-    call ale#engine#ManageDirectory(a:buffer, l:temporary_directory)
-    " Write the buffer out to a file.
-    let l:lines = getbufline(a:buffer, 1, '$')
-    call ale#util#Writefile(a:buffer, l:lines, a:temporary_file)
-
-    return 1
+    " TODO: Emit deprecation warning here later.
+    return ale#command#EscapeCommandPart(a:command_part)
 endfunction
 
 " Run a job.
@@ -517,7 +447,7 @@ function! s:RunJob(options) abort
     \   l:executable,
     \   l:command,
     \   l:read_buffer,
-    \   function('s:CreateTemporaryFileForJob'),
+    \   v:null,
     \)
 
     if l:file_created
diff --git a/autoload/ale/fix.vim b/autoload/ale/fix.vim
index 59502933..b13878eb 100644
--- a/autoload/ale/fix.vim
+++ b/autoload/ale/fix.vim
@@ -66,11 +66,17 @@ function! ale#fix#ApplyQueuedFixes() abort
 endfunction
 
 function! ale#fix#ApplyFixes(buffer, output) abort
-    call ale#fix#RemoveManagedFiles(a:buffer)
-
     let l:data = g:ale_fix_buffer_data[a:buffer]
     let l:data.output = a:output
     let l:data.changes_made = l:data.lines_before != l:data.output
+    let l:data.done = 1
+
+    call ale#command#RemoveManagedFiles(a:buffer)
+
+    if !bufexists(a:buffer)
+        " Remove the buffer data when it doesn't exist.
+        call remove(g:ale_fix_buffer_data, a:buffer)
+    endif
 
     if l:data.changes_made && bufexists(a:buffer)
         let l:lines = getbufline(a:buffer, 1, '$')
@@ -83,13 +89,6 @@ function! ale#fix#ApplyFixes(buffer, output) abort
         endif
     endif
 
-    if !bufexists(a:buffer)
-        " Remove the buffer data when it doesn't exist.
-        call remove(g:ale_fix_buffer_data, a:buffer)
-    endif
-
-    let l:data.done = 1
-
     " We can only change the lines of a buffer which is currently open,
     " so try and apply the fixes to the current buffer.
     call ale#fix#ApplyQueuedFixes()
@@ -146,50 +145,6 @@ function! s:HandleExit(job_id, exit_code) abort
     \})
 endfunction
 
-function! ale#fix#ManageDirectory(buffer, directory) abort
-    call add(g:ale_fix_buffer_data[a:buffer].temporary_directory_list, a:directory)
-endfunction
-
-function! ale#fix#RemoveManagedFiles(buffer) abort
-    if !has_key(g:ale_fix_buffer_data, a:buffer)
-        return
-    endif
-
-    " We can't delete anything in a sandbox, so wait until we escape from
-    " it to delete temporary files and directories.
-    if ale#util#InSandbox()
-        return
-    endif
-
-    " Delete directories like `rm -rf`.
-    " Directories are handled differently from files, so paths that are
-    " intended to be single files can be set up for automatic deletion without
-    " accidentally deleting entire directories.
-    for l:directory in g:ale_fix_buffer_data[a:buffer].temporary_directory_list
-        call delete(l:directory, 'rf')
-    endfor
-
-    let g:ale_fix_buffer_data[a:buffer].temporary_directory_list = []
-endfunction
-
-function! s:CreateTemporaryFileForJob(input, buffer, temporary_file) abort
-    if empty(a:temporary_file)
-        " There is no file, so we didn't create anything.
-        return 0
-    endif
-
-    let l:temporary_directory = fnamemodify(a:temporary_file, ':h')
-    " Create the temporary directory for the file, unreadable by 'other'
-    " users.
-    call mkdir(l:temporary_directory, '', 0750)
-    " Automatically delete the directory later.
-    call ale#fix#ManageDirectory(a:buffer, l:temporary_directory)
-    " Write the buffer out to a file.
-    call ale#util#Writefile(a:buffer, a:input, a:temporary_file)
-
-    return 1
-endfunction
-
 function! s:RunJob(options) abort
     let l:buffer = a:options.buffer
     let l:command = a:options.command
@@ -223,7 +178,7 @@ function! s:RunJob(options) abort
     \   '',
     \   l:command,
     \   l:read_buffer,
-    \   function('s:CreateTemporaryFileForJob', [l:input]),
+    \   l:input,
     \)
 
     let l:command = ale#job#PrepareCommand(l:buffer, l:command)
@@ -469,8 +424,13 @@ function! ale#fix#Fix(buffer, fixing_flag, ...) abort
         call ale#job#Stop(l:job_id)
     endfor
 
+    " Mark the buffer as `done` so files can be removed.
+    if has_key(g:ale_fix_buffer_data, a:buffer)
+        let g:ale_fix_buffer_data[a:buffer].done = 1
+    endif
+
     " Clean up any files we might have left behind from a previous run.
-    call ale#fix#RemoveManagedFiles(a:buffer)
+    call ale#command#RemoveManagedFiles(a:buffer)
     call ale#fix#InitBufferData(a:buffer, a:fixing_flag)
 
     silent doautocmd <nomodeline> User ALEFixPre
diff --git a/autoload/ale/lsp_linter.vim b/autoload/ale/lsp_linter.vim
index d92dae7e..306a2cf1 100644
--- a/autoload/ale/lsp_linter.vim
+++ b/autoload/ale/lsp_linter.vim
@@ -182,7 +182,7 @@ function! ale#lsp_linter#StartLSP(buffer, linter) abort
 
         let l:command = ale#linter#GetCommand(a:buffer, a:linter)
         " Format the command, so %e can be formatted into it.
-        let l:command = ale#command#FormatCommand(a:buffer, l:executable, l:command, 0, {-> 0})[1]
+        let l:command = ale#command#FormatCommand(a:buffer, l:executable, l:command, 0, v:false)[1]
         let l:command = ale#job#PrepareCommand(a:buffer, l:command)
         let l:ready = ale#lsp#StartProgram(l:conn_id, l:executable, l:command)
     endif
diff --git a/doc/ale.txt b/doc/ale.txt
index ac71ab83..ddc5a8a4 100644
--- a/doc/ale.txt
+++ b/doc/ale.txt
@@ -2598,26 +2598,26 @@ ale#Queue(delay, [linting_flag, buffer_number])                   *ale#Queue()*
   is broken, or when developing ALE itself.
 
 
-ale#engine#CreateDirectory(buffer)               *ale#engine#CreateDirectory()*
+ale#command#CreateDirectory(buffer)             *ale#command#CreateDirectory()*
 
   Create a new temporary directory with a unique name, and manage that
-  directory with |ale#engine#ManageDirectory()|, so it will be removed as soon
+  directory with |ale#command#ManageDirectory()|, so it will be removed as soon
   as possible.
 
   It is advised to only call this function from a callback function for
   returning a linter command to run.
 
 
-ale#engine#CreateFile(buffer)                         *ale#engine#CreateFile()*
+ale#command#CreateFile(buffer)                       *ale#command#CreateFile()*
 
   Create a new temporary file with a unique name, and manage that file with
-  |ale#engine#ManageFile()|, so it will be removed as soon as possible.
+  |ale#command#ManageFile()|, so it will be removed as soon as possible.
 
   It is advised to only call this function from a callback function for
   returning a linter command to run.
 
 
-ale#engine#EscapeCommandPart(command_part)     *ale#engine#EscapeCommandPart()*
+ale#command#EscapeCommandPart(command_part)   *ale#command#EscapeCommandPart()*
 
   Given a |String|, return a |String| with all `%` characters replaced with
   `%%` instead. This function can be used to escape strings which are
@@ -2626,6 +2626,35 @@ ale#engine#EscapeCommandPart(command_part)     *ale#engine#EscapeCommandPart()*
   specially.
 
 
+ale#command#ManageFile(buffer, filename)             *ale#command#ManageFile()*
+
+  Given a buffer number for a buffer currently running some linting tasks
+  and a filename, register a filename with ALE for automatic deletion after
+  linting is complete, or when Vim exits.
+
+  If Vim exits suddenly, ALE will try its best to remove temporary files, but
+  ALE cannot guarantee with absolute certainty that the files will be removed.
+  It is advised to create temporary files in the operating system's managed
+  temporary file directory, such as with |tempname()|.
+
+  Directory names should not be given to this function. ALE will only delete
+  files and symlinks given to this function. This is to prevent entire
+  directories from being accidentally deleted, say in cases of writing
+  `dir . '/' . filename` where `filename` is actually `''`, etc. ALE instead
+  manages directories separetly with the |ale#command#ManageDirectory| function.
+
+
+ale#command#ManageDirectory(buffer, directory)  *ale#command#ManageDirectory()*
+
+  Like |ale#command#ManageFile()|, but directories and all of their contents
+  will be deleted, akin to `rm -rf directory`, which could lead to loss of
+  data if mistakes are made. This command will also delete any temporary
+  filenames given to it.
+
+  It is advised to use |ale#command#ManageFile()| instead for deleting single
+  files.
+
+
 ale#engine#GetLoclist(buffer)                         *ale#engine#GetLoclist()*
 
   Given a buffer number, this function will return the list of problems
@@ -2642,35 +2671,6 @@ ale#engine#IsCheckingBuffer(buffer)             *ale#engine#IsCheckingBuffer()*
   This function can be used for status lines, tab names, etc.
 
 
-ale#engine#ManageFile(buffer, filename)               *ale#engine#ManageFile()*
-
-  Given a buffer number for a buffer currently running some linting tasks
-  and a filename, register a filename with ALE for automatic deletion after
-  linting is complete, or when Vim exits.
-
-  If Vim exits suddenly, ALE will try its best to remove temporary files, but
-  ALE cannot guarantee with absolute certainty that the files will be removed.
-  It is advised to create temporary files in the operating system's managed
-  temporary file directory, such as with |tempname()|.
-
-  Directory names should not be given to this function. ALE will only delete
-  files and symlinks given to this function. This is to prevent entire
-  directories from being accidentally deleted, say in cases of writing
-  `dir . '/' . filename` where `filename` is actually `''`, etc. ALE instead
-  manages directories separetly with the |ale#engine#ManageDirectory| function.
-
-
-ale#engine#ManageDirectory(buffer, directory)    *ale#engine#ManageDirectory()*
-
-  Like |ale#engine#ManageFile()|, but directories and all of their contents
-  will be deleted, akin to `rm -rf directory`, which could lead to loss of
-  data if mistakes are made. This command will also delete any temporary
-  filenames given to it.
-
-  It is advised to use |ale#engine#ManageFile()| instead for deleting single
-  files.
-
-
 ale#fix#registry#Add(name, func, filetypes, desc, [aliases])
                                                        *ale#fix#registry#Add()*
 
diff --git a/test/test_format_command.vader b/test/test_format_command.vader
index 119c7138..15435326 100644
--- a/test/test_format_command.vader
+++ b/test/test_format_command.vader
@@ -8,7 +8,9 @@ Before:
     AssertEqual 'dummy.txt', fnamemodify(a:filename, ':t')
   endfunction
 
-  function! TestCreateFunc(buffer, temporary_file) abort
+  runtime autoload/ale/command.vim
+
+  function! ale#command#CreateTempFile(buffer, temporary_file, input) abort
     return !empty(a:temporary_file)
   endfunction
 
@@ -17,17 +19,18 @@ After:
   unlet! g:match
 
   delfunction CheckTempFile
-  delfunction TestCreateFunc
+
+  runtime autoload/ale/command.vim
 
 Execute(FormatCommand should do nothing to basic command strings):
   AssertEqual
   \ ['', 'awesome-linter do something', 0],
-  \ ale#command#FormatCommand(bufnr('%'), '', 'awesome-linter do something', 0, function('TestCreateFunc'))
+  \ ale#command#FormatCommand(bufnr('%'), '', 'awesome-linter do something', 0, v:null)
 
 Execute(FormatCommand should handle %%, and ignore other percents):
   AssertEqual
   \ ['', '% %%d %%f %x %', 0],
-  \ ale#command#FormatCommand(bufnr('%'), '', '%% %%%d %%%f %x %', 0, function('TestCreateFunc'))
+  \ ale#command#FormatCommand(bufnr('%'), '', '%% %%%d %%%f %x %', 0, v:null)
 
 Execute(FormatCommand should convert %s to the current filename):
   AssertEqual
@@ -36,10 +39,10 @@ Execute(FormatCommand should convert %s to the current filename):
   \   'foo ' . ale#Escape(expand('%:p')) . ' bar ' . ale#Escape(expand('%:p')),
   \   0,
   \ ],
-  \ ale#command#FormatCommand(bufnr('%'), '', 'foo %s bar %s', 0, function('TestCreateFunc'))
+  \ ale#command#FormatCommand(bufnr('%'), '', 'foo %s bar %s', 0, v:null)
 
 Execute(FormatCommand should convert %t to a new temporary filename):
-  let g:result = ale#command#FormatCommand(bufnr('%'), '', 'foo %t bar %t', 0, function('TestCreateFunc'))
+  let g:result = ale#command#FormatCommand(bufnr('%'), '', 'foo %t bar %t', 0, v:null)
 
   call CheckTempFile(g:result[0])
 
@@ -52,17 +55,22 @@ Execute(FormatCommand should convert %t to a new temporary filename):
   " The two temporary filenames formatted in should be the same.
   AssertEqual g:match[1], g:match[2]
 
+Execute(FormatCommand should not convert %t to a new temporary filename when the input is given as v:false):
+  let g:result = ale#command#FormatCommand(bufnr('%'), '', 'foo %t bar %t', 0, v:false)
+
+  AssertEqual ['', 'foo %t bar %t', 0], g:result
+
 Execute(FormatCommand should signal that files are created when temporary files are needed):
   AssertEqual
   \ 1,
-  \ ale#command#FormatCommand(bufnr('%'), '', 'foo %t', 0, function('TestCreateFunc'))[2]
+  \ ale#command#FormatCommand(bufnr('%'), '', 'foo %t', 0, v:null)[2]
 
   AssertEqual
   \ 0,
-  \ ale#command#FormatCommand(bufnr('%'), '', 'foo %s', 0, function('TestCreateFunc'))[2]
+  \ ale#command#FormatCommand(bufnr('%'), '', 'foo %s', 0, v:null)[2]
 
 Execute(FormatCommand should let you combine %s and %t):
-  let g:result = ale#command#FormatCommand(bufnr('%'), '', 'foo %t bar %s', 0, function('TestCreateFunc'))
+  let g:result = ale#command#FormatCommand(bufnr('%'), '', 'foo %t bar %s', 0, v:null)
 
   call CheckTempFile(g:result[0])
 
@@ -79,30 +87,30 @@ Execute(FormatCommand should replace %e with the escaped executable):
   if has('win32')
     AssertEqual
     \ ['', 'foo foo', 0],
-    \ ale#command#FormatCommand(bufnr('%'), 'foo', '%e %e', 0, function('TestCreateFunc'))
+    \ ale#command#FormatCommand(bufnr('%'), 'foo', '%e %e', 0, v:null)
     AssertEqual
     \ ['', '"foo bar"', 0],
-    \ ale#command#FormatCommand(bufnr('%'), 'foo bar', '%e', 0, function('TestCreateFunc'))
+    \ ale#command#FormatCommand(bufnr('%'), 'foo bar', '%e', 0, v:null)
     AssertEqual
     \ ['', '%e %e', 0],
-    \ ale#command#FormatCommand(bufnr('%'), '', '%e %e', 0, function('TestCreateFunc'))
+    \ ale#command#FormatCommand(bufnr('%'), '', '%e %e', 0, v:null)
   else
     AssertEqual
     \ ['', '''foo'' ''foo''', 0],
-    \ ale#command#FormatCommand(bufnr('%'), 'foo', '%e %e', 0, function('TestCreateFunc'))
+    \ ale#command#FormatCommand(bufnr('%'), 'foo', '%e %e', 0, v:null)
     AssertEqual
     \ ['', '''foo bar''', 0],
-    \ ale#command#FormatCommand(bufnr('%'), 'foo bar', '%e', 0, function('TestCreateFunc'))
+    \ ale#command#FormatCommand(bufnr('%'), 'foo bar', '%e', 0, v:null)
     AssertEqual
     \ ['', '%e %e', 0],
-    \ ale#command#FormatCommand(bufnr('%'), '', '%e %e', 0, function('TestCreateFunc'))
+    \ ale#command#FormatCommand(bufnr('%'), '', '%e %e', 0, v:null)
   endif
 
 Execute(EscapeCommandPart should escape all percent signs):
   AssertEqual '%%s %%t %%%% %%s %%t %%%%', ale#engine#EscapeCommandPart('%s %t %% %s %t %%')
 
 Execute(EscapeCommandPart should pipe in temporary files appropriately):
-  let g:result = ale#command#FormatCommand(bufnr('%'), '', 'foo bar', 1, function('TestCreateFunc'))
+  let g:result = ale#command#FormatCommand(bufnr('%'), '', 'foo bar', 1, v:null)
 
   call CheckTempFile(g:result[0])
 
@@ -110,7 +118,7 @@ Execute(EscapeCommandPart should pipe in temporary files appropriately):
   Assert !empty(g:match), 'No match found! Result was: ' . g:result[1]
   AssertEqual ale#Escape(g:result[0]), g:match[1]
 
-  let g:result = ale#command#FormatCommand(bufnr('%'), '', 'foo bar %t', 1, function('TestCreateFunc'))
+  let g:result = ale#command#FormatCommand(bufnr('%'), '', 'foo bar %t', 1, v:null)
 
   call CheckTempFile(g:result[0])
 
diff --git a/test/test_sandbox_execution.vader b/test/test_sandbox_execution.vader
index 5a4974ba..cf994ce8 100644
--- a/test/test_sandbox_execution.vader
+++ b/test/test_sandbox_execution.vader
@@ -59,7 +59,7 @@ Execute(ALE shouldn't blow up if file cleanup happens in a sandbox):
   \ 'temporary_file_list': ['/tmp/foo'],
   \ 'temporary_directory_list': ['/tmp/bar'],
   \}
-  sandbox call ale#engine#RemoveManagedFiles(3)
+  sandbox call ale#command#RemoveManagedFiles(3)
 
   AssertEqual ['/tmp/foo'], g:ale_buffer_info[3].temporary_file_list
   AssertEqual ['/tmp/bar'], g:ale_buffer_info[3].temporary_directory_list
diff --git a/test/test_temporary_file_management.vader b/test/test_temporary_file_management.vader
index 4847706a..b25da7ac 100644
--- a/test/test_temporary_file_management.vader
+++ b/test/test_temporary_file_management.vader
@@ -13,21 +13,21 @@ Before:
     " We are registering a temporary file, so we should delete it.
     let g:filename = tempname()
     call writefile(['foo'], g:filename)
-    call ale#engine#ManageFile(a:buffer, g:filename)
+    call ale#command#ManageFile(a:buffer, g:filename)
 
     " We are registering this directory appropriately, so we should delete
     " the whole thing.
     let g:directory = tempname()
     call mkdir(g:directory)
     call writefile(['foo'], g:directory . '/bar')
-    call ale#engine#ManageDirectory(a:buffer, g:directory)
+    call ale#command#ManageDirectory(a:buffer, g:directory)
 
     " We are registering this directory as temporary file, so we
     " shouldn't delete it.
     let g:preserved_directory = tempname()
     call mkdir(g:preserved_directory)
     call writefile(['foo'], g:preserved_directory . '/bar')
-    call ale#engine#ManageFile(a:buffer, g:preserved_directory)
+    call ale#command#ManageFile(a:buffer, g:preserved_directory)
 
     return g:command
   endfunction
@@ -42,6 +42,7 @@ Before:
   \ 'callback': 'TestCallback',
   \ 'command_callback': 'TestCommandCallback',
   \})
+  call ale#command#ClearData()
 
 After:
   Restore
@@ -58,6 +59,7 @@ After:
   delfunction TestCommandCallback
   delfunction TestCallback
   call ale#linter#Reset()
+  call ale#command#ClearData()
 
 Given foobar (Some imaginary filetype):
   foo
@@ -95,11 +97,11 @@ Execute(ALE should delete managed files when the buffer is removed):
   Assert !isdirectory(g:directory), 'The temporary directory was not deleted'
   Assert isdirectory(g:preserved_directory), 'The tempoary directory was not kept'
 
-Execute(ALE should create and delete directories for ale#engine#CreateDirectory()):
+Execute(ALE should create and delete directories for ale#command#CreateDirectory()):
   call ale#engine#InitBufferInfo(bufnr('%'))
 
-  let b:dir = ale#engine#CreateDirectory(bufnr('%'))
-  let b:dir2 = ale#engine#CreateDirectory(bufnr('%'))
+  let b:dir = ale#command#CreateDirectory(bufnr('%'))
+  let b:dir2 = ale#command#CreateDirectory(bufnr('%'))
 
   Assert isdirectory(b:dir), 'The directory was not created'
 
@@ -117,16 +119,26 @@ Execute(ALE should create and delete directories for ale#engine#CreateDirectory(
   Assert !isdirectory(b:dir), 'The directory was not deleted'
   Assert !isdirectory(b:dir2), 'The second directory was not deleted'
 
-Execute(ale#engine#ManageFile should add the file even if the buffer info hasn't be set yet):
-  let g:ale_buffer_info = {}
-  call ale#engine#ManageFile(bufnr(''), '/foo/bar')
-  AssertEqual
-  \ ['/foo/bar'],
-  \ g:ale_buffer_info[bufnr('')].temporary_file_list
+Execute(ale#command#ManageFile should add the file even if the buffer info hasn't be set yet):
+  call ale#command#ManageFile(bufnr(''), '/foo/bar')
 
-Execute(ale#engine#ManageDirectory should add the directory even if the buffer info hasn't be set yet):
-  let g:ale_buffer_info = {}
-  call ale#engine#ManageDirectory(bufnr(''), '/foo/bar')
   AssertEqual
-  \ ['/foo/bar'],
-  \ g:ale_buffer_info[bufnr('')].temporary_directory_list
+  \ {
+  \   bufnr(''): {
+  \     'file_list': ['/foo/bar'],
+  \     'directory_list': [],
+  \   },
+  \ },
+  \ ale#command#GetData()
+
+Execute(ale#command#ManageDirectory should add the directory even if the buffer info hasn't be set yet):
+  call ale#command#ManageDirectory(bufnr(''), '/foo/bar')
+
+  AssertEqual
+  \ {
+  \   bufnr(''): {
+  \     'file_list': [],
+  \     'directory_list': ['/foo/bar'],
+  \   },
+  \ },
+  \ ale#command#GetData()