diff --git a/autoload/ale.vim b/autoload/ale.vim
index 7cf1def6..5efe15ab 100644
--- a/autoload/ale.vim
+++ b/autoload/ale.vim
@@ -53,9 +53,17 @@ function! ale#Queue(delay, ...) abort
         let s:lint_timer = -1
     endif
 
-    let l:linters = ale#linter#Get(&filetype)
-    if len(l:linters) == 0
-        " There are no linters to lint with, so stop here.
+    let l:buffer = bufnr('')
+    let l:linters = ale#linter#Get(getbufvar(l:buffer, '&filetype'))
+
+    " Don't set up buffer data and so on if there are no linters to run.
+    if empty(l:linters)
+        " If we have some previous buffer data, then stop any jobs currently
+        " running and clear everything.
+        if has_key(g:ale_buffer_info, l:buffer)
+            call ale#engine#RunLinters(l:buffer, [], 1)
+        endif
+
         return
     endif
 
@@ -68,16 +76,16 @@ function! ale#Queue(delay, ...) abort
 endfunction
 
 function! ale#Lint(...) abort
-    if ale#ShouldDoNothing()
-        return
-    endif
-
     " Get the buffer number linting was queued for.
     " or else take the current one.
     let l:buffer = len(a:0) > 1 && a:1 == s:lint_timer
     \   ? s:queued_buffer_number
     \   : bufnr('%')
 
+    if ale#ShouldDoNothing()
+        return
+    endif
+
     " Use the filetype from the buffer
     let l:linters = ale#linter#Get(getbufvar(l:buffer, '&filetype'))
     let l:should_lint_file = 0
@@ -89,27 +97,7 @@ function! ale#Lint(...) abort
         let l:should_lint_file = filereadable(expand('#' . l:buffer . ':p'))
     endif
 
-    " Initialise the buffer information if needed.
-    call ale#engine#InitBufferInfo(l:buffer)
-
-    " Clear the new loclist again, so we will work with all new items.
-    let g:ale_buffer_info[l:buffer].new_loclist = []
-
-    if l:should_lint_file
-        " Clear loclist items for files if we are checking files again.
-        let g:ale_buffer_info[l:buffer].lint_file_loclist = []
-    else
-        " Otherwise, don't run any `lint_file` linters
-        " We will continue running any linters which are currently checking
-        " the file, and the items will be mixed together with any new items.
-        call filter(l:linters, '!v:val.lint_file')
-    endif
-
-    call ale#engine#StopCurrentJobs(l:buffer, l:should_lint_file)
-
-    for l:linter in l:linters
-        call ale#engine#Invoke(l:buffer, l:linter)
-    endfor
+    call ale#engine#RunLinters(l:buffer, l:linters, l:should_lint_file)
 endfunction
 
 " Reset flags indicating that files should be checked for all buffers.
diff --git a/autoload/ale/cleanup.vim b/autoload/ale/cleanup.vim
deleted file mode 100644
index 4701b960..00000000
--- a/autoload/ale/cleanup.vim
+++ /dev/null
@@ -1,19 +0,0 @@
-" Author: w0rp <devw0rp@gmail.com>
-" Description: Utility functions related to cleaning state.
-
-function! ale#cleanup#Buffer(buffer) abort
-    if has_key(g:ale_buffer_info, a:buffer)
-        call ale#engine#RemoveManagedFiles(a:buffer)
-
-        " When buffers are removed, clear all of the jobs.
-        call ale#engine#StopCurrentJobs(a:buffer, 1)
-
-        " Clear delayed highlights for a buffer being removed.
-        if g:ale_set_highlights
-            call ale#highlight#UnqueueHighlights(a:buffer)
-            call ale#highlight#RemoveHighlights([])
-        endif
-
-        call remove(g:ale_buffer_info, a:buffer)
-    endif
-endfunction
diff --git a/autoload/ale/engine.vim b/autoload/ale/engine.vim
index fa26a37a..1b32dc85 100644
--- a/autoload/ale/engine.vim
+++ b/autoload/ale/engine.vim
@@ -46,6 +46,14 @@ function! ale#engine#InitBufferInfo(buffer) abort
     endif
 endfunction
 
+" Return 1 if ALE is busy checking a given buffer
+function! ale#engine#IsCheckingBuffer(buffer) abort
+    let l:info = get(g:ale_buffer_info, a:buffer, {})
+
+    return get(l:info, 'waiting_for_tsserver') == 1
+    \|| !empty(get(l:info, 'job_list'))
+endfunction
+
 " Register a temporary file to be managed with the ALE engine for
 " a current job run.
 function! ale#engine#ManageFile(buffer, filename) abort
@@ -69,9 +77,7 @@ function! ale#engine#CreateDirectory(buffer) abort
 endfunction
 
 function! ale#engine#RemoveManagedFiles(buffer) abort
-    if !has_key(g:ale_buffer_info, a:buffer)
-        return
-    endif
+    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.
@@ -80,21 +86,25 @@ function! ale#engine#RemoveManagedFiles(buffer) abort
     endif
 
     " Delete files with a call akin to a plan `rm` command.
-    for l:filename in g:ale_buffer_info[a:buffer].temporary_file_list
-        call delete(l:filename)
-    endfor
+    if has_key(l:info, 'temporary_file_list')
+        for l:filename in l:info.temporary_file_list
+            call delete(l:filename)
+        endfor
 
-    let g:ale_buffer_info[a:buffer].temporary_file_list = []
+        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.
-    for l:directory in g:ale_buffer_info[a:buffer].temporary_directory_list
-        call delete(l:directory, 'rf')
-    endfor
+    if has_key(l:info, 'temporary_directory_list')
+        for l:directory in l:info.temporary_directory_list
+            call delete(l:directory, 'rf')
+        endfor
 
-    let g:ale_buffer_info[a:buffer].temporary_directory_list = []
+        let l:info.temporary_directory_list = []
+    endif
 endfunction
 
 function! s:GatherOutput(job_id, line) abort
@@ -118,34 +128,11 @@ function! s:HandleLoclist(linter_name, buffer, loclist) abort
     " for efficient lookup of the messages in the cursor handler.
     call sort(g:ale_buffer_info[a:buffer].loclist, 'ale#util#LocItemCompare')
 
-    let l:linting_is_done = empty(g:ale_buffer_info[a:buffer].job_list)
-    \   && !get(g:ale_buffer_info[a:buffer], 'waiting_for_tsserver', 0)
-
-    if l:linting_is_done
-        " Automatically remove all managed temporary files and directories
-        " now that all jobs have completed.
-        call ale#engine#RemoveManagedFiles(a:buffer)
-
-        " Figure out which linters are still enabled, and remove
-        " problems for linters which are no longer enabled.
-        let l:name_map = {}
-
-        for l:linter in ale#linter#Get(getbufvar(a:buffer, '&filetype'))
-            let l:name_map[l:linter.name] = 1
-        endfor
-
-        call filter(
-        \   g:ale_buffer_info[a:buffer].loclist,
-        \   'get(l:name_map, v:val.linter_name)',
-        \)
+    if ale#ShouldDoNothing()
+        return
     endif
 
     call ale#engine#SetResults(a:buffer, g:ale_buffer_info[a:buffer].loclist)
-
-    if l:linting_is_done
-        " Call user autocommands. This allows users to hook into ALE's lint cycle.
-        silent doautocmd User ALELint
-    endif
 endfunction
 
 function! s:HandleExit(job_id, exit_code) abort
@@ -217,10 +204,7 @@ function! s:HandleLSPResponse(response) abort
 endfunction
 
 function! ale#engine#SetResults(buffer, loclist) abort
-    let l:info = get(g:ale_buffer_info, a:buffer, {})
-    let l:job_list = get(l:info, 'job_list', [])
-    let l:waiting_for_tsserver = get(l:info, 'waiting_for_tsserver', 0)
-    let l:linting_is_done = empty(l:job_list) && !l:waiting_for_tsserver
+    let l:linting_is_done = !ale#engine#IsCheckingBuffer(a:buffer)
 
     " Set signs first. This could potentially fix some line numbers.
     " The List could be sorted again here by SetSigns.
@@ -254,6 +238,15 @@ function! ale#engine#SetResults(buffer, loclist) abort
         " This will only do something meaningful if we're in normal mode.
         call ale#cursor#EchoCursorWarning()
     endif
+
+    if l:linting_is_done
+        " Automatically remove all managed temporary files and directories
+        " now that all jobs have completed.
+        call ale#engine#RemoveManagedFiles(a:buffer)
+
+        " Call user autocommands. This allows users to hook into ALE's lint cycle.
+        silent doautocmd User ALELint
+    endif
 endfunction
 
 function! s:RemapItemTypes(type_map, loclist) abort
@@ -371,6 +364,9 @@ function! s:CreateTemporaryFileForJob(buffer, temporary_file) abort
     return 1
 endfunction
 
+" Run a job.
+"
+" Returns 1 when the job was started successfully.
 function! s:RunJob(options) abort
     let l:command = a:options.command
     let l:buffer = a:options.buffer
@@ -379,6 +375,10 @@ function! s:RunJob(options) abort
     let l:next_chain_index = a:options.next_chain_index
     let l:read_buffer = a:options.read_buffer
 
+    if empty(l:command)
+        return 0
+    endif
+
     let [l:temporary_file, l:command] = ale#command#FormatCommand(l:buffer, l:command, l:read_buffer)
 
     if s:CreateTemporaryFileForJob(l:buffer, l:temporary_file)
@@ -457,6 +457,8 @@ function! s:RunJob(options) abort
 
         call l:job_options.exit_cb(l:job_id, v:shell_error)
     endif
+
+    return l:job_id != 0
 endfunction
 
 " Determine which commands to run for a link in a command chain, or
@@ -516,11 +518,6 @@ function! ale#engine#ProcessChain(buffer, linter, chain_index, input) abort
         let l:command = ale#linter#GetCommand(a:buffer, a:linter)
     endif
 
-    if empty(l:command)
-        " Don't run any jobs if the command is an empty string.
-        return {}
-    endif
-
     return {
     \   'command': l:command,
     \   'buffer': a:buffer,
@@ -534,16 +531,10 @@ endfunction
 function! s:InvokeChain(buffer, linter, chain_index, input) abort
     let l:options = ale#engine#ProcessChain(a:buffer, a:linter, a:chain_index, a:input)
 
-    if !empty(l:options)
-        call s:RunJob(l:options)
-    elseif empty(g:ale_buffer_info[a:buffer].job_list)
-        " If we cancelled running a command, and we have no jobs in progress,
-        " then delete the managed temporary files now.
-        call ale#engine#RemoveManagedFiles(a:buffer)
-    endif
+    return s:RunJob(l:options)
 endfunction
 
-function! ale#engine#StopCurrentJobs(buffer, include_lint_file_jobs) abort
+function! s:StopCurrentJobs(buffer, include_lint_file_jobs) abort
     let l:info = get(g:ale_buffer_info, a:buffer, {})
     let l:new_job_list = []
 
@@ -562,9 +553,6 @@ function! ale#engine#StopCurrentJobs(buffer, include_lint_file_jobs) abort
 
     " Update the List, so it includes only the jobs we still need.
     let l:info.job_list = l:new_job_list
-    " Ignore current LSP commands.
-    " We should consider cancelling them in future.
-    let l:info.lsp_command_list = []
 endfunction
 
 function! s:CheckWithTSServer(buffer, linter, executable) abort
@@ -584,7 +572,7 @@ function! s:CheckWithTSServer(buffer, linter, executable) abort
             call ale#history#Add(a:buffer, 'failed', l:id, l:command)
         endif
 
-        return
+        return 0
     endif
 
     if ale#lsp#OpenTSServerDocumentIfNeeded(l:id, a:buffer)
@@ -603,21 +591,88 @@ function! s:CheckWithTSServer(buffer, linter, executable) abort
     if l:request_id != 0
         let l:info.waiting_for_tsserver = 1
     endif
+
+    return l:request_id != 0
 endfunction
 
-function! ale#engine#Invoke(buffer, linter) abort
+function! s:RemoveProblemsForDisabledLinters(buffer, linters) abort
+    " Figure out which linters are still enabled, and remove
+    " problems for linters which are no longer enabled.
+    let l:name_map = {}
+
+    for l:linter in a:linters
+        let l:name_map[l:linter.name] = 1
+    endfor
+
+    call filter(
+    \   get(g:ale_buffer_info[a:buffer], 'loclist', []),
+    \   'get(l:name_map, v:val.linter_name)',
+    \)
+endfunction
+
+" Run a linter for a buffer.
+"
+" Returns 1 if the linter was successfully run.
+function! s:RunLinter(buffer, linter) abort
     if empty(a:linter.lsp) || a:linter.lsp ==# 'tsserver'
         let l:executable = ale#linter#GetExecutable(a:buffer, a:linter)
 
         " Run this program if it can be executed.
         if s:IsExecutable(l:executable)
             if a:linter.lsp ==# 'tsserver'
-                call s:CheckWithTSServer(a:buffer, a:linter, l:executable)
-            else
-                call s:InvokeChain(a:buffer, a:linter, 0, [])
+                return s:CheckWithTSServer(a:buffer, a:linter, l:executable)
             endif
+
+            return s:InvokeChain(a:buffer, a:linter, 0, [])
         endif
     endif
+
+    return 0
+endfunction
+
+function! ale#engine#RunLinters(buffer, linters, should_lint_file) abort
+    " Initialise the buffer information if needed.
+    call ale#engine#InitBufferInfo(a:buffer)
+    call s:StopCurrentJobs(a:buffer, a:should_lint_file)
+    call s:RemoveProblemsForDisabledLinters(a:buffer, a:linters)
+
+    let l:any_linter_ran = 0
+
+    for l:linter in a:linters
+        " Skip linters for checking files if we shouldn't check the file.
+        if l:linter.lint_file && !a:should_lint_file
+            continue
+        endif
+
+        if s:RunLinter(a:buffer, l:linter)
+            let l:any_linter_ran = 1
+        endif
+    endfor
+
+    " If we didn't manage to start checking the buffer with anything,
+    " and there's nothing running currently for the buffer, then clear the
+    " results.
+    "
+    " We need to use both checks, as we run some tests synchronously.
+    if !l:any_linter_ran && !ale#engine#IsCheckingBuffer(a:buffer)
+        call ale#engine#SetResults(a:buffer, [])
+    endif
+endfunction
+
+" Clean up a buffer.
+"
+" This function will stop all current jobs for the buffer,
+" clear the state of everything, and remove the Dictionary for managing
+" the buffer.
+function! ale#engine#Cleanup(buffer) abort
+    call ale#engine#RunLinters(a:buffer, [], 1)
+
+    if g:ale_set_highlights
+        call ale#highlight#UnqueueHighlights(a:buffer)
+        call ale#highlight#RemoveHighlights([])
+    endif
+
+    call remove(g:ale_buffer_info, a:buffer)
 endfunction
 
 " Given a buffer number, return the warnings and errors for a given buffer.
diff --git a/autoload/ale/highlight.vim b/autoload/ale/highlight.vim
index 2f7bf5a5..b7255b53 100644
--- a/autoload/ale/highlight.vim
+++ b/autoload/ale/highlight.vim
@@ -67,27 +67,11 @@ function! s:GetALEMatches() abort
     return filter(getmatches(), 'v:val.group =~# ''^ALE''')
 endfunction
 
-function! s:GetCurrentMatchIDs(loclist) abort
-    let l:current_id_map = {}
-
-    for l:item in a:loclist
-        for l:id in get(l:item, 'match_id_list', [])
-            let l:current_id_map[l:id] = 1
-        endfor
-    endfor
-
-    return l:current_id_map
-endfunction
-
 " Given a loclist for current items to highlight, remove all highlights
 " except these which have matching loclist item entries.
 function! ale#highlight#RemoveHighlights(loclist) abort
-    let l:current_id_map = s:GetCurrentMatchIDs(a:loclist)
-
     for l:match in s:GetALEMatches()
-        if !has_key(l:current_id_map, l:match.id)
-            call matchdelete(l:match.id)
-        endif
+        call matchdelete(l:match.id)
     endfor
 endfunction
 
@@ -100,9 +84,6 @@ function! ale#highlight#UpdateHighlights() abort
         call ale#highlight#RemoveHighlights(l:loclist)
     endif
 
-    " Remove anything with a current match_id
-    call filter(l:loclist, '!has_key(v:val, ''match_id_list'')')
-
     " Restore items from the map of hidden items,
     " if we don't have some new items to set already.
     if empty(l:loclist) && has_key(s:buffer_restore_map, l:buffer)
@@ -132,10 +113,7 @@ function! ale#highlight#UpdateHighlights() abort
 
             " Set all of the positions, which are chunked into Lists which
             " are as large as will be accepted by matchaddpos.
-            "
-            " We will remember the IDs we set, so we can preserve some
-            " highlights when linting buffers after linting files.
-            let l:item.match_id_list = map(
+            call map(
             \   ale#highlight#CreatePositions(l:line, l:col, l:end_line, l:end_col),
             \   'matchaddpos(l:group, v:val)'
             \)
@@ -148,14 +126,6 @@ function! ale#highlight#BufferHidden(buffer) abort
 
     " Remember loclist items, so they can be restored later.
     if !empty(l:loclist)
-        " Remove match_ids, as they must be re-calculated when buffers are
-        " shown again.
-        for l:item in l:loclist
-            if has_key(l:item, 'match_id_list')
-                call remove(l:item, 'match_id_list')
-            endif
-        endfor
-
         let s:buffer_restore_map[a:buffer] = filter(
         \   copy(l:loclist),
         \   'v:val.bufnr == a:buffer && v:val.col > 0'
diff --git a/autoload/ale/test.vim b/autoload/ale/test.vim
index 7f06ae91..bfc716de 100644
--- a/autoload/ale/test.vim
+++ b/autoload/ale/test.vim
@@ -15,5 +15,9 @@ function! ale#test#SetFilename(path) abort
         let l:dir = getcwd()
     endif
 
-    silent noautocmd execute 'file ' . fnameescape(ale#path#Simplify(l:dir . '/' . a:path))
+    let l:full_path = ale#path#IsAbsolute(a:path)
+    \   ? a:path
+    \   : l:dir . '/' . a:path
+
+    silent noautocmd execute 'file ' . fnameescape(ale#path#Simplify(l:full_path))
 endfunction
diff --git a/plugin/ale.vim b/plugin/ale.vim
index 58ab1ece..50735753 100644
--- a/plugin/ale.vim
+++ b/plugin/ale.vim
@@ -293,10 +293,9 @@ function! s:ALEToggle() abort
         " Make sure the buffer number is a number, not a string,
         " otherwise things can go wrong.
         for l:buffer in map(keys(g:ale_buffer_info), 'str2nr(v:val)')
-            " Stop jobs and delete stored buffer data
-            call ale#cleanup#Buffer(l:buffer)
-            " Clear signs, loclist, quicklist
-            call ale#engine#SetResults(l:buffer, [])
+            " Stop all jobs and clear the results for everything, and delete
+            " all of the data we stored for the buffer.
+            call ale#engine#Cleanup(l:buffer)
         endfor
 
         " Remove highlights for the current buffer now.
@@ -368,7 +367,7 @@ nnoremap <silent> <Plug>(ale_fix) :ALEFix<Return>
 augroup ALECleanupGroup
     autocmd!
     " Clean up buffers automatically when they are unloaded.
-    autocmd BufUnload * call ale#cleanup#Buffer(expand('<abuf>'))
+    autocmd BufUnload * call ale#engine#Cleanup(str2nr(expand('<abuf>')))
 augroup END
 
 " Backwards Compatibility
diff --git a/test/command_callback/test_javac_command_callback.vader b/test/command_callback/test_javac_command_callback.vader
index 2f0bc50e..706839e4 100644
--- a/test/command_callback/test_javac_command_callback.vader
+++ b/test/command_callback/test_javac_command_callback.vader
@@ -8,7 +8,7 @@ After:
   call ale#linter#Reset()
   " We need to clean up the buffer to remove the temporary directories created
   " for the command.
-  call ale#cleanup#Buffer(bufnr(''))
+  call ale#engine#Cleanup(bufnr(''))
   let g:ale_java_javac_options = ''
   let g:ale_java_javac_classpath = ''
 
@@ -63,7 +63,7 @@ Execute(The javac callback should combine discovered classpaths and manual ones)
   \ 'Invalid command string: ' . b:command
 
 Execute(The javac callback should detect source directories):
-  call ale#cleanup#Buffer(bufnr(''))
+  call ale#engine#Cleanup(bufnr(''))
   :e! java_paths/src/main/java/com/something/dummy
   call ale#engine#InitBufferInfo(bufnr(''))
 
@@ -73,7 +73,7 @@ Execute(The javac callback should detect source directories):
   \ 'Invalid command string: ' . b:command
 
 Execute(The javac callback should combine detected source directories and classpaths):
-  call ale#cleanup#Buffer(bufnr(''))
+  call ale#engine#Cleanup(bufnr(''))
   :e! java_paths/src/main/java/com/something/dummy
   call ale#engine#InitBufferInfo(bufnr(''))
 
diff --git a/test/test_ale_toggle.vader b/test/test_ale_toggle.vader
index 3546ad71..202d8a35 100644
--- a/test/test_ale_toggle.vader
+++ b/test/test_ale_toggle.vader
@@ -11,7 +11,6 @@ Before:
   \ 'valid': 1,
   \}]
   let g:expected_groups = [
-  \ 'ALEBufferFixGroup',
   \ 'ALECleanupGroup',
   \ 'ALECursorGroup',
   \ 'ALEHighlightBufferGroup',
@@ -43,7 +42,10 @@ Before:
     for l:line in split(l:output, "\n")
       let l:match = matchlist(l:line, '^ALE[a-zA-Z]\+Group')
 
+      " We don't care about checking for the completion or fixing groups here.
       if !empty(l:match)
+      \&& l:match[0] !=# 'ALECompletionGroup'
+      \&& l:match[0] !=# 'ALEBufferFixGroup'
         call add(l:results, l:match[0])
       endif
     endfor
@@ -94,15 +96,17 @@ Execute(ALEToggle should reset everything and then run again):
   \ [{'group': 'ALEError', 'pos1': [2, 3, 1]}],
   \ map(getmatches(), '{''group'': v:val.group, ''pos1'': v:val.pos1}')
   AssertEqual g:expected_groups, ParseAuGroups()
+  AssertEqual [{'lnum': 2, 'bufnr': bufnr(''), 'col': 3, 'linter_name': 'testlinter', 'vcol': 0, 'nr': -1, 'type': 'E', 'text': 'foo bar', 'sign_id': 1000001}], g:ale_buffer_info[bufnr('')].loclist
 
   " Now Toggle ALE off.
   ALEToggle
 
   " Everything should be cleared.
-  AssertEqual [], getloclist(0)
-  AssertEqual [], ale#sign#FindCurrentSigns(bufnr('%'))
-  AssertEqual [], getmatches()
-  AssertEqual ['ALEBufferFixGroup', 'ALECleanupGroup', 'ALEHighlightBufferGroup'], ParseAuGroups()
+  Assert !has_key(g:ale_buffer_info, bufnr('')), 'The g:ale_buffer_info Dictionary was not removed'
+  AssertEqual [], getloclist(0), 'The loclist was not cleared'
+  AssertEqual [], ale#sign#FindCurrentSigns(bufnr('%')), 'The signs were not cleared'
+  AssertEqual [], getmatches(), 'The highlights were not cleared'
+  AssertEqual ['ALECleanupGroup', 'ALEHighlightBufferGroup'], ParseAuGroups()
 
   " Toggle ALE on, everything should be set up and run again.
   ALEToggle
@@ -114,3 +118,4 @@ Execute(ALEToggle should reset everything and then run again):
   \ [{'group': 'ALEError', 'pos1': [2, 3, 1]}],
   \ map(getmatches(), '{''group'': v:val.group, ''pos1'': v:val.pos1}')
   AssertEqual g:expected_groups, ParseAuGroups()
+  AssertEqual [{'lnum': 2, 'bufnr': bufnr(''), 'col': 3, 'linter_name': 'testlinter', 'vcol': 0, 'nr': -1, 'type': 'E', 'text': 'foo bar', 'sign_id': 1000001}], g:ale_buffer_info[bufnr('')].loclist
diff --git a/test/test_errors_removed_after_filetype_changed.vader b/test/test_errors_removed_after_filetype_changed.vader
new file mode 100644
index 00000000..0498a501
--- /dev/null
+++ b/test/test_errors_removed_after_filetype_changed.vader
@@ -0,0 +1,58 @@
+Before:
+  Save g:ale_run_synchronously
+
+  let b:old_filetype = &filetype
+  let g:ale_run_synchronously = 1
+
+  noautocmd let &filetype = 'foobar'
+
+  function! TestCallback(buffer, output)
+    return [{'text': 'x', 'lnum': 1}]
+  endfunction
+
+  call ale#linter#Define('foobar', {
+  \ 'name': 'buffer_linter',
+  \ 'callback': 'TestCallback',
+  \ 'executable': 'true',
+  \ 'command': 'true',
+  \ 'read_buffer': 0,
+  \})
+
+  call ale#linter#Define('foobar2', {
+  \ 'name': 'buffer_linter',
+  \ 'callback': 'TestCallback',
+  \ 'executable': 'true',
+  \ 'command': 'true',
+  \ 'read_buffer': 0,
+  \})
+
+After:
+  Restore
+
+  noautocmd let &filetype = b:old_filetype
+  unlet b:old_filetype
+  delfunction TestCallback
+
+  if has_key(g:ale_buffer_info, bufnr(''))
+    call remove(g:ale_buffer_info, bufnr(''))
+  endif
+
+  call ale#Queue(0)
+
+Execute(Error should be removed when the filetype changes to something else we cannot check):
+  call ale#Queue(0)
+
+  AssertEqual 1, len(getloclist(0))
+
+  noautocmd let &filetype = 'foobar2'
+
+  call ale#Queue(0)
+
+  " We should get some items from the second filetype.
+  AssertEqual 1, len(getloclist(0))
+
+  noautocmd let &filetype = 'xxx'
+
+  call ale#Queue(0)
+
+  AssertEqual 0, len(getloclist(0))
diff --git a/test/test_highlight_placement.vader b/test/test_highlight_placement.vader
index a134916f..3fa45ed2 100644
--- a/test/test_highlight_placement.vader
+++ b/test/test_highlight_placement.vader
@@ -22,6 +22,18 @@ Before:
     \]
   endfunction
 
+  " We don't care what the IDs are, just that we have some matches.
+  " The IDs are generated.
+  function! GetMatchesWithoutIDs() abort
+    let l:list = getmatches()
+
+    for l:item in l:list
+      call remove(l:item, 'id')
+    endfor
+
+    return l:list
+  endfunction
+
   call ale#linter#Define('testft', {
   \ 'name': 'x',
   \ 'executable': 'echo',
@@ -51,33 +63,11 @@ Execute(Highlights should be set when a linter runs):
 
   AssertEqual
   \ [
-  \   {'group': 'ALEError', 'id': 4, 'priority': 10, 'pos1': [1, 1, 1]},
-  \   {'group': 'ALEWarning', 'id': 5, 'priority': 10, 'pos1': [2, 1, 1]},
-  \   {'group': 'ALEError', 'id': 6, 'priority': 10, 'pos1': [3, 5, 1]}
+  \   {'group': 'ALEError', 'priority': 10, 'pos1': [1, 1, 1]},
+  \   {'group': 'ALEWarning', 'priority': 10, 'pos1': [2, 1, 1]},
+  \   {'group': 'ALEError', 'priority': 10, 'pos1': [3, 5, 1]}
   \ ],
-  \ getmatches()
-
-  AssertEqual [[4], [5], [6]], map(copy(g:ale_buffer_info[bufnr('')].loclist), 'v:val.match_id_list')
-
-Execute(Existing highlights should be kept):
-  call matchaddpos('ALEError', [[1, 2, 1]], 10, 347)
-  call matchaddpos('ALEWarning', [[2, 2, 1]], 10, 348)
-
-  call ale#highlight#SetHighlights(bufnr('%'), [
-  \ {'bufnr': bufnr('%'), 'match_id_list': [347], 'type': 'E', 'lnum': 1, 'col': 2},
-  \ {'bufnr': bufnr('%'), 'match_id_list': [348], 'type': 'W', 'lnum': 2, 'col': 2},
-  \ {'bufnr': bufnr('%'), 'type': 'E', 'lnum': 3, 'col': 2},
-  \ {'bufnr': bufnr('%'), 'type': 'W', 'lnum': 4, 'col': 1},
-  \])
-
-  AssertEqual
-  \ [
-  \   {'group': 'ALEError', 'id': 347, 'priority': 10, 'pos1': [1, 2, 1]},
-  \   {'group': 'ALEWarning', 'id': 348, 'priority': 10, 'pos1': [2, 2, 1]},
-  \   {'group': 'ALEError', 'id': 7, 'priority': 10, 'pos1': [3, 2, 1]},
-  \   {'group': 'ALEWarning', 'id': 8, 'priority': 10, 'pos1': [4, 1, 1]},
-  \ ],
-  \ getmatches()
+  \ GetMatchesWithoutIDs()
 
 " This test is important for preventing ALE from showing highlights for
 " the wrong files.
@@ -89,12 +79,12 @@ Execute(Highlights set by ALE should be removed when buffer cleanup is done):
   \])
 
   AssertEqual
-  \ [{'group': 'ALEError', 'id': 9, 'priority': 10, 'pos1': [3, 2, 1]}],
-  \ getmatches()
+  \ [{'group': 'ALEError', 'priority': 10, 'pos1': [3, 2, 1]}],
+  \ GetMatchesWithoutIDs()
 
-  call ale#cleanup#Buffer(bufnr('%'))
+  call ale#engine#Cleanup(bufnr('%'))
 
-  AssertEqual [], getmatches()
+  AssertEqual [], GetMatchesWithoutIDs()
 
 Execute(Highlights should be cleared when buffers are hidden):
   call ale#engine#InitBufferInfo(bufnr('%'))
@@ -108,15 +98,15 @@ Execute(Highlights should be cleared when buffers are hidden):
   \ g:ale_buffer_info[bufnr('%')].loclist
   \)
 
-  AssertEqual 1, len(getmatches()), 'The highlights weren''t initially set!'
+  AssertEqual 1, len(GetMatchesWithoutIDs()), 'The highlights weren''t initially set!'
 
   call ale#highlight#BufferHidden(bufnr('%'))
 
-  AssertEqual 0, len(getmatches()), 'The highlights weren''t cleared!'
+  AssertEqual 0, len(GetMatchesWithoutIDs()), 'The highlights weren''t cleared!'
 
   call ale#highlight#UpdateHighlights()
 
-  AssertEqual 1, len(getmatches()), 'The highlights weren''t set again!'
+  AssertEqual 1, len(GetMatchesWithoutIDs()), 'The highlights weren''t set again!'
 
 Execute(Only ALE highlights should be restored when buffers are restored):
   call ale#engine#InitBufferInfo(bufnr('%'))
@@ -131,16 +121,16 @@ Execute(Only ALE highlights should be restored when buffers are restored):
   call matchaddpos('SomeOtherGroup', [[1, 1, 1]])
 
   " We should have one more match here.
-  AssertEqual 2, len(getmatches()), 'The highlights weren''t initially set!'
+  AssertEqual 2, len(GetMatchesWithoutIDs()), 'The highlights weren''t initially set!'
 
   call ale#highlight#BufferHidden(bufnr('%'))
 
-  AssertEqual 0, len(getmatches()), 'The highlights weren''t cleared!'
+  AssertEqual 0, len(GetMatchesWithoutIDs()), 'The highlights weren''t cleared!'
 
   call ale#highlight#UpdateHighlights()
 
   " Only our matches should appear again.
-  AssertEqual 1, len(getmatches()), 'The highlights weren''t set again!'
+  AssertEqual 1, len(GetMatchesWithoutIDs()), 'The highlights weren''t set again!'
 
 Execute(Higlight end columns should set an appropriate size):
   call ale#highlight#SetHighlights(bufnr('%'), [
@@ -150,10 +140,10 @@ Execute(Higlight end columns should set an appropriate size):
 
   AssertEqual
   \ [
-  \   {'group': 'ALEError', 'id': 15, 'priority': 10, 'pos1': [3, 2, 4]},
-  \   {'group': 'ALEWarning', 'id': 16, 'priority': 10, 'pos1': [4, 1, 5]},
+  \   {'group': 'ALEError', 'priority': 10, 'pos1': [3, 2, 4]},
+  \   {'group': 'ALEWarning', 'priority': 10, 'pos1': [4, 1, 5]},
   \ ],
-  \ getmatches()
+  \ GetMatchesWithoutIDs()
 
 Execute(Higlight end columns should set an appropriate size):
   call ale#highlight#SetHighlights(bufnr('%'), [
@@ -168,15 +158,15 @@ Execute(Higlight end columns should set an appropriate size):
 
   AssertEqual
   \ [
-  \   {'group': 'ALEError', 'id': 17, 'priority': 10, 'pos1': [1, 1, 1]},
-  \   {'group': 'ALEError', 'id': 18, 'priority': 10, 'pos1': [2, 1, 1]},
-  \   {'group': 'ALEStyleError', 'id': 19, 'priority': 10, 'pos1': [3, 1, 1]},
-  \   {'group': 'ALEWarning', 'id': 20, 'priority': 10, 'pos1': [4, 1, 1]},
-  \   {'group': 'ALEWarning', 'id': 21, 'priority': 10, 'pos1': [5, 1, 1]},
-  \   {'group': 'ALEStyleWarning', 'id': 22, 'priority': 10, 'pos1': [6, 1, 1]},
-  \   {'group': 'ALEInfo', 'id': 23, 'priority': 10, 'pos1': [7, 1, 1]},
+  \   {'group': 'ALEError', 'priority': 10, 'pos1': [1, 1, 1]},
+  \   {'group': 'ALEError', 'priority': 10, 'pos1': [2, 1, 1]},
+  \   {'group': 'ALEStyleError', 'priority': 10, 'pos1': [3, 1, 1]},
+  \   {'group': 'ALEWarning', 'priority': 10, 'pos1': [4, 1, 1]},
+  \   {'group': 'ALEWarning', 'priority': 10, 'pos1': [5, 1, 1]},
+  \   {'group': 'ALEStyleWarning', 'priority': 10, 'pos1': [6, 1, 1]},
+  \   {'group': 'ALEInfo', 'priority': 10, 'pos1': [7, 1, 1]},
   \ ],
-  \ getmatches()
+  \ GetMatchesWithoutIDs()
 
 Execute(Highlighting should support errors spanning many lines):
   let g:items = [
@@ -189,15 +179,13 @@ Execute(Highlighting should support errors spanning many lines):
   AssertEqual
   \ [
   \   {
-  \     'group': 'ALEError', 'id': 24, 'priority': 10, 'pos1': [1, 1, 1073741824],
+  \     'group': 'ALEError', 'priority': 10, 'pos1': [1, 1, 1073741824],
   \     'pos2': [2], 'pos3': [3], 'pos4': [4], 'pos5': [5], 'pos6': [6],
   \     'pos7': [7], 'pos8': [8],
   \   },
   \   {
-  \     'group': 'ALEError', 'id': 25, 'priority': 10,
+  \     'group': 'ALEError', 'priority': 10,
   \     'pos1': [9], 'pos2': [10, 1, 3]
   \   },
   \ ],
-  \ getmatches()
-
-  AssertEqual [[24, 25]], map(copy(g:items), 'v:val.match_id_list')
+  \ GetMatchesWithoutIDs()
diff --git a/test/test_lint_file_linters.vader b/test/test_lint_file_linters.vader
index a02ecca3..b0dc1eb3 100644
--- a/test/test_lint_file_linters.vader
+++ b/test/test_lint_file_linters.vader
@@ -69,6 +69,10 @@ Before:
   \ 'read_buffer': 0,
   \})
 
+  let g:filename = tempname()
+  call writefile([], g:filename)
+  call ale#test#SetFilename(g:filename)
+
 After:
   Restore
 
@@ -79,6 +83,12 @@ After:
   delfunction LintFileCallback
   delfunction BufferCallback
 
+  if filereadable(g:filename)
+    call delete(g:filename)
+  endif
+
+  unlet g:filename
+
 Given foobar (Some imaginary filetype):
   foo
   bar
@@ -107,6 +117,9 @@ Execute(Running linters without 'lint_file' should run only buffer linters):
 Execute(Running linters with 'lint_file' should run all linters):
   call ale#ResetLintFileMarkers()
   let g:ale_buffer_info = {}
+
+  Assert filereadable(expand('%:p')), 'The file was not readable'
+
   call ale#Queue(0, 'lint_file')
 
   AssertEqual [
@@ -139,6 +152,9 @@ Execute(Running linters with 'lint_file' should run all linters):
 Execute(Linter errors from files should be kept):
   call ale#ResetLintFileMarkers()
   let g:ale_buffer_info = {}
+
+  Assert filereadable(expand('%:p')), 'The file was not readable'
+
   call ale#Queue(0, 'lint_file')
 
   " Change the results for the buffer callback.
diff --git a/test/test_lint_on_enter_when_file_changed.vader b/test/test_lint_on_enter_when_file_changed.vader
index ff4e7dd5..cfa53878 100644
--- a/test/test_lint_on_enter_when_file_changed.vader
+++ b/test/test_lint_on_enter_when_file_changed.vader
@@ -30,6 +30,8 @@ After:
   call setloclist(0, [])
 
 Execute(The file changed event function should set b:ale_file_changed):
+  let g:ale_lint_on_enter = 0
+
   if has('gui')
     new
   else
diff --git a/test/test_linting_updates_loclist.vader b/test/test_linting_updates_loclist.vader
index 009a4537..19adfa1f 100644
--- a/test/test_linting_updates_loclist.vader
+++ b/test/test_linting_updates_loclist.vader
@@ -65,8 +65,4 @@ Execute(The loclist should be updated after linting is done):
   call ale#engine#WaitForJobs(2000)
 
   AssertEqual ['' . bufnr('%')], keys(g:ale_buffer_info)
-
-  let g:expected_data[0].match_id_list = [getmatches()[0].id]
-  let g:expected_data[1].match_id_list = [getmatches()[1].id]
-
   AssertEqual g:expected_data, g:ale_buffer_info[bufnr('%')].loclist
diff --git a/test/test_temporary_file_management.vader b/test/test_temporary_file_management.vader
index 4eed345c..6d1f0dfd 100644
--- a/test/test_temporary_file_management.vader
+++ b/test/test_temporary_file_management.vader
@@ -84,7 +84,7 @@ Execute(ALE should delete managed files even if no command is run):
 Execute(ALE should delete managed files when the buffer is removed):
   call ale#engine#InitBufferInfo(bufnr('%'))
   call TestCommandCallback(bufnr('%'))
-  call ale#cleanup#Buffer(bufnr('%'))
+  call ale#engine#Cleanup(bufnr('%'))
 
   Assert !filereadable(g:filename), 'The temporary file was not deleted'
   Assert !isdirectory(g:directory), 'The temporary directory was not deleted'
@@ -105,7 +105,7 @@ Execute(ALE should create and delete directories for ale#engine#CreateDirectory(
   " The two directories shouldn't be the same.
   AssertNotEqual b:dir2, b:dir
 
-  call ale#cleanup#Buffer(bufnr('%'))
+  call ale#engine#Cleanup(bufnr('%'))
 
   Assert !isdirectory(b:dir), 'The directory was not deleted'
   Assert !isdirectory(b:dir2), 'The second directory was not deleted'