logic: refresh info generator fixes and tests

* fixed case where "to-index" state of a file has changed and thus the file needs to be re-indexed
* clear and re-index files that depend on changed non-indexed files
* clear and re-index files referenced by unchanged but cleared (due to referencing a changed file) files
* fixed: updated files with changed timestamp that do not have content in the db will now count as changed
* refined refresh info generator tests
* updated checklists for manual project setup tests

testing/project_setup/cpp_empty/checklist.txt

@@ -25,7 +25,7 @@
 * Click "Cancel"
 * Run "2_update.sh"
 * Press "Refresh" button
-* Validate "Files to clear" shows "2"
+* Validate "Files to clear" shows "3"
 * Validate "source files to index" shows "1"
 * Click "Start"
 * Validate Project indexed without error

testing/project_setup/cxx_cbp/checklist.txt

@@ -24,7 +24,7 @@
 * Click "Cancel"
 * Run "2_update.sh"
 * Press "Refresh" button
-* Validate "Files to clear" shows "2"
+* Validate "Files to clear" shows "3"
 * Validate "source files to index" shows "1"
 * Click "Start"
 * Validate Project indexed without error

testing/project_setup/cxx_cdb/checklist.txt

@@ -24,7 +24,7 @@
 * Click "Cancel"
 * Run "2_update.sh"
 * Press "Refresh" button
-* Validate "Files to clear" shows "2"
+* Validate "Files to clear" shows "3"
 * Validate "source files to index" shows "1"
 * Click "Start"
 * Validate Project indexed without error

testing/project_setup/cxx_sonargraph_manual/checklist.txt

@@ -23,7 +23,7 @@
 * Click "Cancel"
 * Run "2_update.sh"
 * Press "Refresh" button
-* Validate "Files to clear" shows "2"
+* Validate "Files to clear" shows "3"
 * Validate "source files to index" shows "1"
 * Click "Start"
 * Validate Project indexed without error