Fix a bug where the sign column was not closed some of the time, etc.

autoload/ale/engine.vim

@@ -460,6 +460,7 @@ function! s:RunJob(options) abort
     let l:output_stream = a:options.output_stream
     let l:next_chain_index = a:options.next_chain_index
     let l:read_buffer = a:options.read_buffer
+    let l:info = g:ale_buffer_info[l:buffer]
 
     if empty(l:command)
         return 0
@@ -515,8 +516,11 @@ function! s:RunJob(options) abort
     " Only proceed if the job is being run.
     if l:job_id
         " Add the job to the list of jobs, so we can track them.
-        call add(g:ale_buffer_info[l:buffer].job_list, l:job_id)
-        call add(g:ale_buffer_info[l:buffer].active_linter_list, l:linter.name)
+        call add(l:info.job_list, l:job_id)
+
+        if index(l:info.active_linter_list, l:linter.name) < 0
+            call add(l:info.active_linter_list, l:linter.name)
+        endif
 
         let l:status = 'started'
         " Store the ID for the job in the map to read back again.
@@ -531,7 +535,7 @@ function! s:RunJob(options) abort
     if g:ale_history_enabled
         call ale#history#Add(l:buffer, l:status, l:job_id, l:command)
     else
-        let g:ale_buffer_info[l:buffer].history = []
+        let l:info.history = []
     endif
 
     if get(g:, 'ale_run_synchronously') == 1
@@ -624,6 +628,7 @@ endfunction
 function! s:StopCurrentJobs(buffer, include_lint_file_jobs) abort
     let l:info = get(g:ale_buffer_info, a:buffer, {})
     let l:new_job_list = []
+    let l:new_active_linter_list = []
 
     for l:job_id in get(l:info, 'job_list', [])
         let l:job_info = get(s:job_info_map, l:job_id, {})
@@ -634,15 +639,23 @@ function! s:StopCurrentJobs(buffer, include_lint_file_jobs) abort
                 call remove(s:job_info_map, l:job_id)
             else
                 call add(l:new_job_list, l:job_id)
+                " Linters with jobs still running are still active.
+                call add(l:new_active_linter_list, l:job_info.linter.name)
             endif
         endif
     endfor
 
+    " Remove duplicates from the active linter list.
+    call uniq(sort(l:new_active_linter_list))
+
     " Update the List, so it includes only the jobs we still need.
     let l:info.job_list = l:new_job_list
+    " Update the active linter list, clearing out anything not running.
+    let l:info.active_linter_list = l:new_active_linter_list
 endfunction
 
 function! s:CheckWithLSP(buffer, linter) abort
+    let l:info = g:ale_buffer_info[a:buffer]
     let l:lsp_details = ale#linter#StartLSP(
     \   a:buffer,
     \   a:linter,
@@ -665,7 +678,9 @@ function! s:CheckWithLSP(buffer, linter) abort
     let l:request_id = ale#lsp#Send(l:id, l:change_message, l:root)
 
     if l:request_id != 0
-        call add(g:ale_buffer_info[a:buffer].active_linter_list, a:linter.name)
+        if index(l:info.active_linter_list, a:linter.name) < 0
+            call add(l:info.active_linter_list, a:linter.name)
+        endif
     endif
 
     return l:request_id != 0

test/test_lint_file_linters.vader

@@ -79,6 +79,10 @@ Before:
   call ale#test#SetFilename(g:filename)
 
 After:
+  if !g:ale_run_synchronously
+    call ale#engine#WaitForJobs(2000)
+  endif
+
   Restore
 
   unlet! b:ale_save_event_fired
@@ -267,3 +271,19 @@ Execute(b:ale_save_event_fired should be set to 0 when results are set):
   call ale#engine#SetResults(bufnr(''), [])
 
   AssertEqual 0, b:ale_save_event_fired
+
+Execute(lint_file linters should stay running after checking without them):
+  let g:ale_run_synchronously = 0
+
+  " Run all linters, then just the buffer linters.
+  call ale#Queue(0, 'lint_file')
+  call ale#Queue(0)
+
+  " The lint_file linter should still be running.
+  AssertEqual
+  \ ['lint_file_linter', 'buffer_linter'],
+  \ g:ale_buffer_info[bufnr('')].active_linter_list
+  " We should have 1 job for each linter.
+  AssertEqual 2, len(g:ale_buffer_info[bufnr('')].job_list)
+
+  call ale#engine#WaitForJobs(2000)