Subset of a possible fix:
```diff
diff --git a/src/build.c b/src/build.c
index 56ec9d613..3d94a683f 100644
--- a/src/build.c
+++ b/src/build.c
@@ -1898,7 +1898,7 @@ static RowWidgets *build_add_dialog_row(GeanyDocument 
*doc, GtkTable *table, gui
                        GTK_FILL | GTK_EXPAND, entry_x_padding, 
entry_y_padding);
        }
        column++;
-       clearicon = gtk_image_new_from_stock(GTK_STOCK_CLEAR, 
GTK_ICON_SIZE_MENU);
+       clearicon = gtk_image_new_from_icon_name("edit-clear-symbolic", 
GTK_ICON_SIZE_MENU);
        clear = gtk_button_new();
        gtk_button_set_image(GTK_BUTTON(clear), clearicon);
        g_signal_connect(clear, "clicked", G_CALLBACK(on_clear_dialog_row), 
roww);
@@ -1995,7 +1995,7 @@ GtkWidget *build_commands_table(GeanyDocument *doc, 
GeanyBuildSource dst, BuildT
        }
        gtk_table_attach(table, fields->fileregex, DC_ENTRIES + 1, DC_CLEAR, 
row, row + 1, GTK_FILL,
                GTK_FILL | GTK_EXPAND, entry_x_padding, entry_y_padding);
-       clearicon = gtk_image_new_from_stock(GTK_STOCK_CLEAR, 
GTK_ICON_SIZE_MENU);
+       clearicon = gtk_image_new_from_icon_name("edit-clear-symbolic", 
GTK_ICON_SIZE_MENU);
        clear = gtk_button_new();
        gtk_button_set_image(GTK_BUTTON(clear), clearicon);
        g_signal_connect_swapped(clear, "clicked",
@@ -2029,7 +2029,7 @@ GtkWidget *build_commands_table(GeanyDocument *doc, 
GeanyBuildSource dst, BuildT
        }
        gtk_table_attach(table, fields->nonfileregex, DC_ENTRIES + 1, DC_CLEAR, 
row, row + 1, GTK_FILL,
                GTK_FILL | GTK_EXPAND, entry_x_padding, entry_y_padding);
-       clearicon = gtk_image_new_from_stock(GTK_STOCK_CLEAR, 
GTK_ICON_SIZE_MENU);
+       clearicon = gtk_image_new_from_icon_name("edit-clear-symbolic", 
GTK_ICON_SIZE_MENU);
        clear = gtk_button_new();
        gtk_button_set_image(GTK_BUTTON(clear), clearicon);
        g_signal_connect_swapped(clear, "clicked",
diff --git a/src/notebook.c b/src/notebook.c
index ec00d3e96..df6f44f9d 100644
--- a/src/notebook.c
+++ b/src/notebook.c
@@ -746,7 +746,7 @@ gint notebook_new_tab(GeanyDocument *this)
                gtk_button_set_focus_on_click(GTK_BUTTON(btn), FALSE);
                gtk_widget_set_name(btn, "geany-close-tab-button");
 
-               image = gtk_image_new_from_stock(GTK_STOCK_CLOSE, 
GTK_ICON_SIZE_MENU);
+               image = gtk_image_new_from_icon_name("window-close-symbolic", 
GTK_ICON_SIZE_MENU);
                gtk_container_add(GTK_CONTAINER(btn), image);
 
                align = gtk_alignment_new(1.0, 0.5, 0.0, 0.0);
diff --git a/src/ui_utils.c b/src/ui_utils.c
index 34b26bc62..602d87080 100644
--- a/src/ui_utils.c
+++ b/src/ui_utils.c
@@ -1601,7 +1601,7 @@ static void entry_clear_icon_release_cb(GtkEntry *entry, 
gint icon_pos,
 GEANY_API_SYMBOL
 void ui_entry_add_clear_icon(GtkEntry *entry)
 {
-       g_object_set(entry, "secondary-icon-stock", GTK_STOCK_CLEAR,
+       g_object_set(entry, "secondary-icon-name", "edit-clear-symbolic",
                "secondary-icon-activatable", TRUE, NULL);
        g_signal_connect(entry, "icon-release", 
G_CALLBACK(entry_clear_icon_release_cb), NULL);
 }
```

IIUC in theory GTK icons should fall back on the non-symbolic version if the 
symbolic one is missing.  Not sure if it plays any better if there's the same 
"one is there but not in the correct size" issue though.

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