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In there, you will see the following structure (or at least a subset of it):
/
LogFiles
Application
<instance>-<pid>-<ticks>.txt // application (nodejs/dotnet/php) traces
DetailedError
ErrorPage####.htm // error details
Git
trace
trace.xml // Trace generated during git deployments
<instance>-<guid>.txt // kudu related traces
deployment
<instance>-<guid>.txt // deployment related traces
http
RawLogs
<logfile>.log // iis http log. iis buffers and flushes every 60sec.
W3SVC#####
fr####.xml // IIS fail request traces
freb.xsl
site
wwwroot
hello.htm // The files that are live in your app
repository // Your repo, including working files (i.e. not bare)
.git
HEAD, index and other git files
deployments
[commit id 1]
log.xml // The deployment log, similar to what the protal shows
status.xml // The status of the deployment (success/failure)
manifest // The list of files that were deployed
[commit id 2]
...
.ssh
config // This contains config to disable strict host checking
id_rsa // private key in PEM format
known_hosts // known hosts have been accepted
kuduservice
Used when your site uses private kudu bits