Updating to latest codebase FAIL, please help

I have been getting this error on all three servers that I have:

warning: unable to access ‘/root/.config/git/attributes’: Permission denied
warning: unable to access ‘/root/.config/git/ignore’: Permission denied
error: Your local changes to the following files would be overwritten by merge:
.editorconfig
.gitignore
.travis.yml
LibreNMS/Alert/Template.php
LibreNMS/Alert/Transport/Alertmanager.php
LibreNMS/Alert/Transport/Canopsis.php
LibreNMS/Alert/Transport/Elasticsearch.php
LibreNMS/Alert/Transport/Mattermost.php
LibreNMS/Authentication/ADAuthorizationAuthorizer.php
LibreNMS/Authentication/ActiveDirectoryAuthorizer.php
LibreNMS/Authentication/LdapAuthorizationAuthorizer.php
LibreNMS/Authentication/LdapAuthorizer.php
LibreNMS/Authentication/MysqlAuthorizer.php
LibreNMS/Component.php
LibreNMS/Exceptions/DatabaseConnectException.php
LibreNMS/Interfaces/Alert/Transport.php
LibreNMS/OS/Ruckuswireless.php
LibreNMS/Util/Laravel.php
LibreNMS/Util/ModuleTestHelper.php
LibreNMS/Util/Url.php
LibreNMS/Validations/Database.php
LibreNMS/Validations/Rrd.php
README.md
app/ApiClients/RipeApi.php
app/Checks.php
app/Console/Commands/BashCompletionCommand.php
app/Console/Kernel.php
app/Exceptions/Handler.php
app/Http/Controllers/Auth/RegisterController.php
app/Http/Controllers/Table/FdbTablesController.php
app/Http/Kernel.php
app/Http/Middleware/EncryptCookies.php
app/Http/Middleware/TrimStrings.php
app/Http/Middleware/VerifyCsrfToken.php
app/Models/Device.php
app/Models/PortsFdb.php
app/Models/User.php
app/Providers/AppServiceProvider.php
app/Providers/EventServiceProvider.php
artisan
bootstrap/app.php
composer.json
composer.lock
config/app.php
config/auth.php
config/broadcasting.php
config/cache.php
config/database.php
config/debugbar.php
config/filesystems.php
config/librenms.php
config/mail.php
config/queue.php
config/services.php
config/session.php
config/snmptraps.php
config/toastr.php
config/trustedproxy.php
config/view.php
daily.php
daily.sh
database/factories/ModelFactory.php
database/migrations/2018_07_03_091314_create_alert_schedulables_table.php
database/migrations/2018_07_03_091322_add_foreign_keys_to_sensors_to_state_indexes_table.php
database/seeds/DatabaseSeeder.php
doc/Alerting/Creating-Transport.md
doc/Alerting/Templates.md
doc/Alerting/Transports.md
doc/Extensions/Authentication.md
doc/Extensions/Smokeping.md
doc/Installation/Installation-CentOS-6-Apache-Nginx.md
doc/Installation/Installation-CentOS-7-Apache.md
doc/Installation/Installation-CentOS-7-Nginx.md
doc/Installation/Installation-Ubuntu-1404-Apache.md
doc/Installation/Installation-Ubuntu-1404-Lighttpd.md
doc/Installation/Installation-Ubuntu-1404-Nginx.md
doc/Installation/Installation-Ubuntu-1604-Apache.md
doc/Installation/Installation-Ubuntu-1604-Nginx.md
doc/Installation/Installation-Ubuntu-1804-Apache.md
doc/Installation/Installation-Ubuntu-1804-Nginx.md
doc/Installation/index.md
doc/Support/Adding-a-Device.md
doc/Support/Configuration.md
doc/Support/Discovery Support.md
doc/Support/Example-Hardware-Setup.md
doc/Support/FAQ.md
doc/Support/Features.md
html/ajax_ossuggest.php
html/images/os/pfsense.svg
html/includes/forms/convert-template.inc.php
html/includes/graphs/graph.inc.php
html/legacy_index.php
html/pages/device/port/fdb.inc.php
html/pages/device/ports/fdb.inc.php
html/pages/search/fdb.inc.php
includes/alerts.inc.php
includes/defaults.inc.php
includes/definitions/alcoma-almp.yaml
includes/definitions/cyberpower.yaml
includes/definitions/discovery/junos.yaml
includes/definitions/discovery/saf-cfm.yaml
includes/definitions/discovery/vrp.yaml
includes/definitions/edgeswitch.yaml
includes/definitions/jetstream.yaml
includes/definitions/marathonups.yaml
includes/definitions/mypoweros.yaml
includes/definitions/perle.yaml
includes/definitions/ruckuswireless.yaml
includes/definitions/serverscheck.yaml
includes/definitions/voss.yaml
includes/discovery/fdb-table.inc.php
includes/discovery/sensors/state/voss.inc.php
includes/functions.php
includes/init.php
includes/polling/os/dkt.inc.php
includes/polling/os/edgeos.inc.php
includes/polling/os/ruckuswireless.inc.php
includes/polling/ports.inc.php
includes/syslog.php
mibs/ruckus/RUCKUS-PRODUCTS-MIB
mibs/ruckus/RUCKUS-ROOT-MIB
mibs/ruckus/RUCKUS-TC-MIB
misc/db_schema.yaml
misc/macros.json
misc/notifications.rss
misc/os_schema.json
package.json
phpunit.xml
resources/lang/en/validation.php
resources/views/auth/login-form.blade.php
resources/views/layouts/librenmsv1.blade.php
resources/views/welcome.blade.php
routes/web.php
server.php
storage/framework/cache/.gitignore
tests/AlertingTest.php
tests/AuthSSOTest.php
tests/DBSetupTest.php
tests/DocsTest.php
tests/IpTest.php
tests/LockTest.php
tests/RrdtoolTest.php
tests/TestCase.php
tests/bootstrap.php
tests/data/edgecos_es3510ma.json
tests/data/junos_ex.json
tests/data/netscaler-sdwan.json
tests/data/ruckuswireless_zd1100.json
tests/data/ruckuswireless_zd1200.json
tests/data/serverscheck.json
tests/module_tables.yaml
tests/snmpsim/edgeos.snmprec
tests/snmpsim/junos.snmprec
tests/snmpsim/junos_ex.snmprec
tests/snmpsim/mypoweros.snmprec
tests/snmpsim/netgear.snmprec
tests/snmpsim/netscaler-sdwan.snmprec
tests/snmpsim/ruckuswireless_zd1100.snmprec
tests/snmpsim/ruckuswireless_zd1200.snmprec
webpack.mix.js
Please, commit your changes or stash them before you can merge.
error: The following untracked working tree files would be overwritten by merge:
LibreNMS/Exceptions/DuskUnsafeException.php
LibreNMS/Exceptions/FilePermissionsException.php
LibreNMS/Exceptions/LdapMissingException.php
LibreNMS/Interfaces/Exceptions/UpgradeableException.php
LibreNMS/OS/FsGbn.php
LibreNMS/OS/FsSwitch.php
LibreNMS/OS/ProtelevisionT1.php
LibreNMS/OS/RuckuswirelessHotzone.php
LibreNMS/OS/RuckuswirelessSz.php
LibreNMS/OS/RuckuswirelessUnleashed.php
LibreNMS/Snmptrap/Handlers/EquipStatusTrap.php
LibreNMS/Snmptrap/Handlers/LogTrap.php
app/Application.php
app/Console/Commands/AddUserCommand.php
app/Console/LnmsCommand.php
app/Events/UserCreated.php
app/Http/Controllers/Auth/VerificationController.php
app/Listeners/MarkNotificationsRead.php
config/hashing.php
config/logging.php
config/tinker.php
database/migrations/2019_02_10_220000_add_dates_to_fdb.php
html/images/logos/maipu.png
html/images/logos/pfsense.svg
html/images/logos/protelevision.png
html/images/logos/sagemcom.svg
html/images/os/fs.svg
html/images/os/osmc.png
html/images/os/protelevision.png
html/images/os/sagemcom.svg
html/images/os/serverscheck.svg
html/svg/403.svg
html/svg/404.svg
html/svg/500.svg
html/svg/503.svg
includes/definitions/compas.yaml
includes/definitions/discovery/ionos.yaml
includes/definitions/discovery/mypoweros.yaml
includes/definitions/discovery/netgear.yaml
includes/definitions/discovery/netscaler-sdwan.yaml
includes/definitions/discovery/nokia-isam.yaml
includes/definitions/discovery/protelevision-t1.yaml
includes/definitions/discovery/ruckuswireless-hotzone.yaml
includes/definitions/discovery/ruckuswireless-unleashed.yaml
includes/definitions/fs-gbn.yaml
includes/definitions/fs-switch.yaml
includes/definitions/ionos.yaml
includes/definitions/nokia-isam.yaml
includes/definitions/protelevision-t1.yaml
includes/definitions/ruckuswireless-hotzone.yaml
includes/definitions/ruckuswireless-sz.yaml
includes/definitions/ruckuswireless-unleashed.yaml
includes/discovery/mempools/fs-gbn.inc.php
includes/discovery/mempools/fs-switch.inc.php
includes/discovery/mempools/mypoweros.inc.php
includes/discovery/mempools/nokia-isam.inc.php
includes/discovery/mempools/ruckuswireless-hotzone.inc.php
includes/discovery/mempools/ruckuswireless-unleashed.inc.php
includes/discovery/mempools/ruckuswireless.inc.php
includes/discovery/sensors/charge/compas.inc.php
includes/discovery/sensors/current/compas.inc.php
includes/discovery/sensors/dbm/nokia-isam.inc.php
includes/discovery/sensors/pre-cache/nokia-isam.inc.php
includes/discovery/sensors/runtime/compas.inc.php
includes/discovery/sensors/state/compas.inc.php
includes/discovery/sensors/state/nokia-isam.inc.php
includes/discovery/sensors/temperature/compas.inc.php
includes/discovery/sensors/temperature/nokia-isam.inc.php
includes/discovery/sensors/voltage/compas.inc.php
includes/polling/mempools/fs-gbn.inc.php
includes/polling/mempools/fs-switch.inc.php
includes/polling/mempools/mypoweros.inc.php
includes/polling/mempools/nokia-isam.inc.php
includes/polling/mempools/ruckuswireless-hotzone.inc.php
includes/polling/mempools/ruckuswireless-unleashed.inc.php
includes/polling/mempools/ruckuswireless.inc.php
includes/polling/os/fs-gbn.inc.php
includes/polling/os/fs-switch.inc.php
includes/polling/os/netscaler-sdwan.inc.php
includes/polling/os/nokia-isam.inc.php
includes/polling/os/protelevision-t1.inc.php
includes/polling/os/ruckuswireless-hotzone.inc.php
includes/polling/os/ruckuswireless-sz.inc.php
includes/polling/os/ruckuswireless-unleashed.inc.php
includes/polling/ports/nokia-isam.inc.php
includes/polling/sensors/state/eds.inc.php
includes/polling/sensors/temperature/eds.inc.php
mibs/MGMD-STD-MIB
mibs/MSTP-MIB
mibs/alpha/SITE-MONITORING-MIB
mibs/citrix/CITRIX-NetScaler-SD-WAN-MIB
mibs/fs/ADMIN-MASTER-MIB
mibs/fs/ERRP-MIB
mibs/fs/GARP-MIB
mibs/fs/GBNDeviceOEM-MIB
mibs/fs/GBNDevicePoe-MIB
mibs/fs/GBNDeviceSWAPI-MIB
mibs/fs/GBNDeviceStack-MIB
mibs/fs/GBNDeviceSwitch-MIB
mibs/fs/GBNL2Dhcp6Snooping-MIB
mibs/fs/GBNL2DhcpSnooping-MIB
mibs/fs/GBNL2PortSecurity-MIB
mibs/fs/GBNL2PppoePlus-MIB
mibs/fs/GBNL2QACL-MIB
mibs/fs/GBNL2Switch-MIB
mibs/fs/GBNL3-MIB
mibs/fs/GBNL3DhcpRelay-MIB
mibs/fs/GBNL3IPPool-MIB
mibs/fs/GBNL3If-MIB
mibs/fs/GBNL3Igmp-MIB
mibs/fs/GBNL3Ospf-MIB
mibs/fs/GBNL3PIM-MIB
mibs/fs/GBNL3Rip-MIB
mibs/fs/GBNL3RouteCommon-MIB
mibs/fs/GBNPlatformChassis-MIB
mibs/fs/GBNPlatformGNLink-MIB
mibs/fs/GBNPlatformOAM-MIB
mibs/fs/GBNPlatformOAMMailalarm-MIB
mibs/fs/GBNPlatformOAMSntpClient-MIB
mibs/fs/GBNPlatformOAMSsh-MIB
mibs/fs/GBNPlatformOAMSyslog-MIB
mibs/fs/GBNPlatformOAMTelnet-MIB
mibs/fs/GBNServiceCM-MIB
mibs/fs/GBNServiceMACAUTHEN-MIB
mibs/fs/GBNServiceRADIUS-MIB
mibs/fs/GBNServiceRMON-MIB
mibs/fs/GBNServiceTACACS-MIB
mibs/fs/LAG-ARCH-MIB
mibs/fs/LLDPPRIVATE-MIB
mibs/fs/MAC-NOTIFICATION-MIB
mibs/fs/NSCRTV-EPON-ALARM-MGM-MIB
mibs/fs/NSCRTV-EPON-IGMP-MGM-MIB
mibs/fs/NSCRTV-EPON-PERFORMANCE-STAT-MIB
mibs/fs/NSCRTV-EPON-QOS-MGM-MIB
mibs/fs/NSCRTV-EPON-SNI-MIB
mibs/fs/NSCRTV-EPON-STP-MGM-MIB
mibs/fs/NSCRTV-EPON-SYSTEM-MIB
mibs/fs/NSCRTV-EPON-VLAN-MGM-MIB
mibs/fs/NSCRTV-EPONEOC-EPON-MIB
mibs/fs/PIM-BSR-MIB
mibs/fs/STP-MIB
mibs/fs/SWITCH
mibs/maipu/MAIPU-SMI
mibs/maipu/MPIOS-MIB
mibs/netgear/NETGEAR-BOXSERVICES-PRIVATE-MIB
mibs/netgear/NETGEAR-REF-MIB
mibs/nokia/ASAM-ALARM-MIB
mibs/nokia/ASAM-EQUIP-MIB
mibs/nokia/ASAM-SYSTEM-MIB
mibs/nokia/ASAM-TC-MIB
mibs/nokia/ITF-MIB
mibs/nokia/ITF-MIB-EXT
mibs/nokia/SFP-MIB
mibs/nokia/SYSTEM-MIB
mibs/perle/PERLE-IOLAN-SDS-MIB
mibs/protelevision/PT-MIB
mibs/protelevision/PT3080-MIB
mibs/ruckus/RUCKUS-CTRL-MIB
mibs/ruckus/RUCKUS-SYSTEM-MIB
mibs/ruckus/RUCKUS-SZ-CONFIG-WLAN-MIB
mibs/ruckus/RUCKUS-SZ-EVENT-MIB
mibs/ruckus/RUCKUS-SZ-SYSTEM-MIB
mibs/ruckus/RUCKUS-SZ-WLAN-MIB
mibs/ruckus/RUCKUS-UNLEASHED-EVENT-MIB
mibs/ruckus/RUCKUS-UNLEASHED-SYSTEM-MIB
mibs/ruckus/RUCKUS-UNLEASHED-WLAN-MIB
mibs/sagemcom/ADR155C-MIB
mibs/sagemcom/ADR2500C-MIB
mibs/sagemcom/ADR63E1-MIB
mibs/sagemcom/EQUIPMENT-MIB
mibs/sagemcom/GIGE-MIB
mibs/sagemcom/LOG-MIB
mibs/sagemcom/PERFORMANCE-MIB
mibs/sagemcom/PPP-BRIDGE-NCP-MIB
mibs/sagemcom/PPP-LCP-MIB
mibs/sagemcom/PROTECTION-MIB
mibs/sagemcom/SAGEM-DR-MIB
mibs/sagemcom/SDH-ETS-MIB
mibs/sagemcom/SESSION-MIB
mibs/sagemcom/SHELF-MIB
mibs/sagemcom/SPRIF-MIB
mibs/sagemcom/XCONNECTION-MIB
resources/js/app.js
resources/js/bootstrap.js
resources/js/components/ExampleComponent.vue
resources/lang/en/commands.php
resources/sass/_variables.scss
resources/sass/app.scss
resources/views/errors/500.blade.php
tests/Browser/LoginTest.php
tests/Browser/Pages/LoginPage.php
tests/Browser/Pages/Page.php
tests/Browser/console/.gitignore
tests/Browser/screenshots/.gitignore
tests/DuskTestCase.php
tests/data/compas.json
tests/data/edgeos.json
tests/data/fs-gbn_2800.json
tests/data/fs-gbn_3800.json
tests/data/fs-switch_5800.json
tests/data/ionos.json
tests/data/jetstream_t1600g-18ts.json
tests/data/junos.json
tests/data/junos_srx3600.json
tests/data/mypoweros.json
tests/data/netgear.json
tests/data/nokia-isam.json
tests/data/protelevision-t1.json
tests/data/ruckuswireless-hotzone.json
tests/data/ruckuswireless-sz.json
tests/data/ruckuswireless-unleashed.json
tests/data/voss_8608.json
tests/data/voss_9012.json
tests/data/vrp_5720-32x-ei.json
tests/snmpsim/compas.snmprec
tests/snmpsim/fs-gbn_2800.snmprec
tests/snmpsim/fs-gbn_3800.snmprec
tests/snmpsim/fs-switch_5800.snmprec
tests/snmpsim/ionos.snmprec
tests/snmpsim/jetstream_t1600g-18ts.snmprec
tests/snmpsim/jetstream_t1600g-28ts.snmprec
tests/snmpsim/jetstream_t1700g-28tq.snmprec
tests/snmpsim/nokia-isam.snmprec
tests/snmpsim/perle_iolanscs.snmprec
tests/snmpsim/protelevision-t1.snmprec
tests/snmpsim/ruckuswireless-hotzone.snmprec
tests/snmpsim/ruckuswireless-sz.snmprec
tests/snmpsim/ruckuswireless-unleashed.snmprec
tests/snmpsim/voss_8608.snmprec
tests/snmpsim/voss_9012.snmprec
tests/snmpsim/vrp_5720-32x-ei.snmprec
Please move or remove them before you can merge.
Aborting

step one sudo/su to the librenms user properly.
su - librenms or sudo -i -u librenms

step two clean up the failed attempt to merge updates with your local changes to LibreNMS system files.
./scripts/github-remove -d

step three update
./daily.sh

step for validate
./validate.php

1 Like

Thanks Murrant

I still get this error message 

Updating to latest codebase FAIL
error: The following untracked working tree files would be overwritten by merge:
config/hashing.php
config/logging.php
config/tinker.php
Please move or remove them before you can merge.

You can safely remove them manually (all 3) and re-run the steps from @murrant.

Perfect, thank you.