OK. I patched the file as indicated. The patch apparently uploads correctly, although the following message is displayed:
Warning: stat(): stat failed for upload/upgrades/patch/SuiteCRM-Upgrade-7.10-to-7.10.1-manifest.php occurred in .../include/UploadStream.php on line 308 [2018-03-11 10:28:22] display_stack_trace caller, file: .../include/utils.php line#: 3533
[L:](:StackTraceErrorHandler)
.../include/UploadStream.php[L:308](:stat)
[L:](UploadStream:url_stat)
.../modules/UpgradeWizard/upload.php[L:152](:copy)
.../modules/UpgradeWizard/index.php[L:297](:require)
.../include/MVC/View/SugarView.php[L:807](:include_once)
.../include/MVC/View/views/view.classic.php[L:74](SugarView:includeClassicFile)
.../include/MVC/View/SugarView.php[L:207](ViewClassic:display)
.../include/MVC/Controller/SugarController.php[L:432](SugarView:process)
.../include/MVC/Controller/SugarController.php[L:375](SugarController:processView)
.../include/MVC/SugarApplication.php[L:109](SugarController:execute)
.../index.php[L:52](SugarApplication:execute)
I don’t understand why the message is there, because the file upload/upgrades/patch/SuiteCRM-Upgrade-7.10-to-7.10.1-manifest.php is indeed present.
Next, the following message is displayed:
Upgrade process will update some files but these files also exist in custom/ folder. Please review the changes before continuing:
include/generic/SugarWidgets/SugarWidgetSubPanelTopSelectContactsButton.php => custom/include/generic/SugarWidgets/SugarWidgetSubPanelTopSelectContactsButton.php
include/generic/SugarWidgets/SugarWidgetSubPanelTopSelectUsersButton.php => custom/include/generic/SugarWidgets/SugarWidgetSubPanelTopSelectUsersButton.php
include/language/en_us.lang.php => custom/include/language/en_us.lang.php
metadata/securitygroups_acl_rolesMetaData.php => custom/metadata/securitygroups_acl_rolesMetaData.php
metadata/securitygroups_defaultsMetaData.php => custom/metadata/securitygroups_defaultsMetaData.php
metadata/securitygroups_recordsMetaData.php => custom/metadata/securitygroups_recordsMetaData.php
modules/Home/language/en_us.lang.php => custom/modules/Home/language/en_us.lang.php
modules/Leads/language/en_us.lang.php => custom/modules/Leads/language/en_us.lang.php
modules/Leads/metadata/detailviewdefs.php => custom/modules/Leads/metadata/detailviewdefs.php
modules/Leads/metadata/editviewdefs.php => custom/modules/Leads/metadata/editviewdefs.php
modules/Opportunities/metadata/detailviewdefs.php => custom/modules/Opportunities/metadata/detailviewdefs.php
modules/Prospects/language/en_us.lang.php => custom/modules/Prospects/language/en_us.lang.php
modules/Prospects/metadata/detailviewdefs.php => custom/modules/Prospects/metadata/detailviewdefs.php
modules/Prospects/metadata/editviewdefs.php => custom/modules/Prospects/metadata/editviewdefs.php
modules/Accounts/metadata/detailviewdefs.php => custom/modules/Accounts/metadata/detailviewdefs.php
modules/ACLRoles/views/view.classic.php => custom/modules/ACLRoles/views/view.classic.php
modules/Connectors/connectors/sources/ext/rest/insideview/mapping.php => custom/modules/Connectors/connectors/sources/ext/rest/insideview/mapping.php
modules/Connectors/metadata/searchdefs.php => custom/modules/Connectors/metadata/searchdefs.php
modules/Contacts/language/en_us.lang.php => custom/modules/Contacts/language/en_us.lang.php
modules/Contacts/metadata/detailviewdefs.php => custom/modules/Contacts/metadata/detailviewdefs.php
modules/Contacts/metadata/editviewdefs.php => custom/modules/Contacts/metadata/editviewdefs.php
modules/Contacts/metadata/SearchFields.php => custom/modules/Contacts/metadata/SearchFields.php
Having no idea at all whether this is normal or not, and how those custom/modules files came to be, I continued.
After the Commit upgrade, in spite of the “Files coped successfully” message, there was a long series of stat failed warnings, similar to the first one (above). But all the files are there. The directories have permissions 755 and the files 644.
The last step in the upgrade resulted in yet another warning:
Warning: exec() has been disabled for security reasons occurred in .../include/utils.php on line 449 [2018-03-11 11:09:43] display_stack_trace caller, file: .../include/utils.php line#: 3533
[L:](:StackTraceErrorHandler)
.../include/utils.php[L:449](:exec)
.../modules/UpgradeWizard/end.php[L:219](:getRunningUser)
.../modules/UpgradeWizard/index.php[L:297](:require)
.../include/MVC/View/SugarView.php[L:831](:include_once)
.../include/MVC/View/views/view.classic.php[L:74](SugarView:includeClassicFile)
.../include/MVC/View/SugarView.php[L:207](ViewClassic:display)
.../include/MVC/Controller/SugarController.php[L:432](SugarView:process)
.../include/MVC/Controller/SugarController.php[L:375](SugarController:processView)
.../include/MVC/SugarApplication.php[L:109](SugarController:execute)
.../index.php[L:52](SugarApplication:execute)
It is indeed true that exec has been disabled. But it is not clear if something has failed and needs to be redone, or if something has failed.
There are NO warnings or errors or mention of failure in the upgrade log.
Bottom line: Things seem to work, although there are a lot of unexplained messages.