It seems that you should add @without_default@ referenced by @ProjectsController#retrieve_default_query@(source:/trunk/app/controllers/projects_controller.rb#L333) and @IssuesController#retrieve_default_query@(source:/trunk/app/controllers/issues_controller.rb#L489) to the query string.
<pre><code class="ruby">
def retrieve_default_query(use_session)
return if params[:query_id].present?
return if api_request?
return if params[:set_filter] && (params.key?(:op) || params.key?(:f))

if params[:without_default].present?
params[:set_filter] = 1
return
end
</code></pre>

Maybe you need to fix the following:
<pre><code class="shell">
% grep -rn "set_filter" * --exclude-dir={vendor,public,tmp,doc,log,test,config/locales,files,coverage,spec,node_modules}
app/models/mailer.rb:567: :set_filter => 1, :assigned_to_id => 'me',
app/models/mailer.rb:570: :set_filter => 1, :sort => 'due_date:asc',
app/models/query.rb:463: params[:set_filter] = 1
app/controllers/issues_controller.rb:487: return if params[:set_filter] && (params.key?(:op) || params.key?(:f))
app/controllers/issues_controller.rb:490: params[:set_filter] = 1
app/controllers/issues_controller.rb:493: if !params[:set_filter] && use_session && session[:issue_query]
app/controllers/queries_controller.rb:87: redirect_to_items(:set_filter => 1)
app/controllers/projects_controller.rb:331: return if params[:set_filter] && (params.key?(:op) || params.key?(:f))
app/controllers/projects_controller.rb:334: params[:set_filter] = 1
app/views/calendars/show.html.erb:5:<%= hidden_field_tag 'set_filter', '1' %>
app/views/calendars/show.html.erb:29: <%= link_to l(:button_clear), { :project_id => @project, :set_filter => 1 }, :class => 'icon icon-reload' %>
app/views/context_menus/issues.html.erb:146: <li><%= context_menu_link l(:button_filter), _project_issues_path(@project, :set_filter => 1, :status_id => "*", :issue_id => @issue_ids.join(","), :c => @columns),
app/views/context_menus/issues.html.erb:163: <li><%= copy_object_url_link(_project_issues_url(@project, set_filter: 1, status_id: '*', issue_id: @issue_ids.join(','))) %></li>
app/views/projects/show.html.erb:71: <%= link_to tracker.name, project_issues_path(@project, :set_filter => 1, :tracker_id => tracker.id), :title => tracker.description %>
app/views/projects/show.html.erb:74: <%= link_to @open_issues_by_tracker[tracker].to_i, project_issues_path(@project, :set_filter => 1, :tracker_id => tracker.id) %>
app/views/projects/show.html.erb:77: <%= link_to (@total_issues_by_tracker[tracker].to_i - @open_issues_by_tracker[tracker].to_i), project_issues_path(@project, :set_filter => 1, :tracker_id => tracker.id, :status_id => 'c') %>
app/views/projects/show.html.erb:80: <%= link_to @total_issues_by_tracker[tracker].to_i, project_issues_path(@project, :set_filter => 1, :tracker_id => tracker.id, :status_id => '*') %>
app/views/projects/show.html.erb:88: <%= link_to l(:label_issue_view_all), project_issues_path(@project, :set_filter => 1) %>
app/views/versions/_issue_counts.html.erb:18: <%= link_to(count[:group], project_issues_path(version.project, :set_filter => 1, :status_id => '*', :fixed_version_id => version, "#{criteria}_id" => count[:group])) %>
app/views/versions/_issue_counts.html.erb:20: <%= link_to(l(:label_none), project_issues_path(version.project, :set_filter => 1, :status_id => '*', :fixed_version_id => version, "#{criteria}_id" => "!*")) %>
app/views/versions/show.html.erb:23: project_issues_path(@version.project, :set_filter => 1, :status_id => '*', :fixed_version_id => @version.id, :c => [:tracker, :status, :subject, :estimated_hours], :t => [:estimated_hours]) %></td>
app/views/versions/show.html.erb:29: project_time_entries_path(@version.project, :set_filter => 1, :"issue.fixed_version_id" => @version.id) %></td>
app/views/queries/_query_form.html.erb:1:<%= hidden_field_tag 'set_filter', '1' %>
app/views/queries/_query_form.html.erb:57: <%= link_to l(:button_clear), { :set_filter => 1, :sort => '', :project_id => @project }, :class => 'icon icon-reload' %>
app/views/imports/_issues_saved_objects.html.erb:7:<p><%= link_to l(:label_issue_view_all), issues_path(:set_filter => 1, :status_id => '*', :issue_id => saved_objects.map(&:id).join(',')) %></p>
app/views/welcome/robots.text.erb:15:Disallow: <%= url_for(issues_path) %>?*set_filter=
app/views/users/show.html.erb:42: issues_path(:set_filter => 1, :assigned_to_id => assigned_to_ids, :sort => sort_cond) %>
app/views/users/show.html.erb:46: issues_path(:set_filter => 1, :assigned_to_id => assigned_to_ids, :sort => sort_cond) %>
app/views/users/show.html.erb:50: issues_path(:set_filter => 1, :status_id => 'c', :assigned_to_id => assigned_to_ids, :sort => sort_cond) %>
app/views/users/show.html.erb:54: issues_path(:set_filter => 1, :status_id => '*', :assigned_to_id => assigned_to_ids, :sort => sort_cond) %>
app/views/users/show.html.erb:60: issues_path(:set_filter => 1, :author_id => @user.id, :sort => sort_cond) %>
app/views/users/show.html.erb:64: issues_path(:set_filter => 1, :author_id => @user.id, :sort => sort_cond) %>
app/views/users/show.html.erb:68: issues_path(:set_filter => 1, :status_id => 'c', :author_id => @user.id, :sort => sort_cond) %>
app/views/users/show.html.erb:72: issues_path(:set_filter => 1, :status_id => '*', :author_id => @user.id, :sort => sort_cond) %>
app/views/gantts/show.html.erb:11:<%= hidden_field_tag 'set_filter', '1' %>
app/views/gantts/show.html.erb:91: <%= link_to l(:button_clear), { :project_id => @project, :set_filter => 1 },
app/helpers/queries_helper.rb:344: elsif api_request? || params[:set_filter] || !use_session ||
app/helpers/queries_helper.rb:417: tags = hidden_field_tag("set_filter", "1", :id => nil)
app/helpers/queries_helper.rb:475: clear_link_param = {:set_filter => 1, :sort => '', :project_id => @project}
app/helpers/queries_helper.rb:498: def link_to_clear_query(params = {:set_filter => 1, :sort => '', :project_id => @project})
app/helpers/reports_helper.rb:44: parameters = {:set_filter => 1, :subproject_id => '!*', field => (row.id || '!*')}.merge(options)
app/helpers/versions_helper.rb:31: options = {:fixed_version_id => version, :set_filter => 1}.merge(options)
app/helpers/issues_helper.rb:172: link_to(total_issues, issues_path(issues_path_attr.merge({:set_filter => true, :status_id => '*'}))),
app/helpers/issues_helper.rb:180: issues_path(issues_path_attr.merge({:set_filter => true, :status_id => 'c'}))
app/helpers/issues_helper.rb:189: issues_path(issues_path_attr.merge({:set_filter => true, :status_id => 'o'}))
</code></pre>

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Maybe it is enough to relax the @set_filter@ if to not include the second condition (@op@ and @f@ params)?
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Marius BALTEANU wrote:
> Maybe it is enough to relax the @set_filter@ if to not include the second condition (@op@ and @f@ params)?

I think that it works properly if only @set_filter@ is judged without the second condition. And I don't think the @without_default@ parameter is needed.

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If we change as I proposed, then the @without_default@ param doesn't make any sense anymore.

I'll wait for some more feedback before I commit this.
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Patch committed.
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relates,Closed,7360,Issue custom query: default query per instance, project and user
relates,Closed,35795,Settings for global and user default custom ProjectQuery