Updates for new repo layout.

_docs/concepts/policy-and-control/mixer-config.md

@@ -302,4 +302,4 @@ manifests:
 
 You can find fully-formed examples of Mixer configuration by visiting the
 [Guides]({{home}}/docs/guides). Here is some [example
-configuration](https://github.com/istio/mixer/blob/master/testdata/config).
+configuration](https://github.com/istio/istio/blob/master/mixer/testdata/config).

_docs/reference/config/mixer/adapters/index.md

@@ -10,5 +10,5 @@ type: markdown
 
 {% include section-index.html %}
 
-To implement a new adapter for Mixer, please refer to the [Adapter Developer's Guide](https://github.com/istio/mixer/blob/master/doc/dev/adapters.md).
+To implement a new adapter for Mixer, please refer to the [Adapter Developer's Guide](https://github.com/istio/istio/blob/master/mixer/doc/dev/adapters.md).
 

_docs/reference/release-notes.md

@@ -65,7 +65,7 @@ rich proxy-side caching and batching for increased performance.
 
 - **New Mixer Adapter Model**. A new adapter composition model makes it easier to extend Mixer by adding whole new classes of adapters via templates. This 
 new model will serve as the foundational building block for many features in the future. See the
-[Adapter Developer's Guide](https://github.com/istio/mixer/blob/master/doc/dev/adapters.md) to learn how
+[Adapter Developer's Guide](https://github.com/istio/istio/blob/master/mixer/doc/dev/adapters.md) to learn how
 to write adapters.
 
 - **Improved Mixer Build Model**. It’s now easier to build a Mixer binary that includes custom adapters.

_docs/setup/consul/install.md

@@ -122,8 +122,7 @@ Part of the sidecar installation should involve setting up appropriate IP
 Table rules to transparently route application's network traffic through
 the Istio sidecars. The IP table script to setup such forwarding can be
 found in the
-[Istio Pilot repository](https://github.com/istio/pilot/blob/master/docker/prepare_proxy.sh). 
+[here](https://github.com/istio/istio/blob/master/pilot/docker/prepare_proxy.sh). 
 
 > Note: This script must be executed before starting the application or
 > the sidecar process. 
-

_docs/setup/eureka/install.md

@@ -102,8 +102,7 @@ service mesh.
 Part of the sidecar installation should involve setting up appropriate IP
 Table rules to transparently route application's network traffic through
 the Istio sidecars. The IP table script to setup such forwarding can be
-found in the
-[Istio Pilot repository](https://github.com/istio/pilot/blob/master/docker/prepare_proxy.sh). 
+found [here](https://github.com/istio/istio/blob/master/pilot/docker/prepare_proxy.sh). 
 
 > Note: This script must be executed before starting the application or
 > the sidecar process. 

_docs/tasks/telemetry/faq.md

@@ -183,4 +183,4 @@ In the 0.2 release, Mixer only supports Zipkin tracing.
 ## How can I write a custom adapter for Mixer ?
 
 To implement a new adapter for Mixer, please refer to the [Adapter Developer's
-Guide](https://github.com/istio/mixer/blob/master/doc/dev/adapters.md).
+Guide](https://github.com/istio/istio/blob/master/mixer/doc/dev/adapters.md).

_faq/where-is-the-documentation.md

@@ -15,7 +15,7 @@ Detailed developer-level documentation is maintained for each component in GitHu
 
 *   [Envoy](https://envoyproxy.github.io/envoy/)
 
-*   [Pilot](https://github.com/istio/pilot/tree/master/doc)
+*   [Pilot](https://github.com/istio/istio/tree/master/pilot/doc)
 
-*   [Mixer](https://github.com/istio/mixer/tree/master/doc)
+*   [Mixer](https://github.com/istio/istio/tree/master/mixer/doc)
 

_posts/2017-05-25-0.1-auth.md

@@ -98,4 +98,7 @@ Istio Auth is part of the broader security story for containers. Red Hat, a part
 
 ## Join us in this journey
 
-Istio Auth is the first step towards providing a full stack of capabilities to protect services with sensitive data from external attacks and insider threats. While the initial version runs on Kubernetes, our goal is to enable Istio Auth to secure services across diverse production environments. We encourage the community to [join us](https://github.com/istio/auth) in making robust service security easy and ubiquitous across different application stacks and runtime platforms. 
+Istio Auth is the first step towards providing a full stack of capabilities to protect services with sensitive data from external attacks and insider
+threats. While the initial version runs on Kubernetes, our goal is to enable Istio Auth to secure services across diverse production environments. We encourage the 
+community to [join us](https://github.com/istio/istio/blob/master/security) in making robust service security easy and ubiquitous across different application 
+stacks and runtime platforms. 

_posts/2017-10-10-0.2-announcement.md

@@ -23,7 +23,10 @@ Today we are happy to announce the 0.2 release which improves stability and perf
 
 * _Automated sidecar injection_: By leveraging the alpha [initializer](https://kubernetes.io/docs/admin/extensible-admission-controllers/#what-are-initializers) feature provided by Kubernetes 1.7, envoy sidecars can now be automatically injected into application deployments when your cluster has the initializer enabled.  This enables you to deploy microservices using `kubectl`, the exact same command that you normally use for deploying the microservices without Istio.
 
-* _Extending Istio_: An improved mixer design that lets vendors write Mixer adapters to implement support for their own systems, such as application management or policy enforcement. The [Mixer adapter guide](https://github.com/istio/mixer/blob/master/doc/dev/adapters.md) can help you easily integrate your solution with Istio. 
+* _Extending Istio_: An improved Mixer design that lets vendors write Mixer adapters to implement support for their own systems, such as application 
+management or policy enforcement. The
+[Mixer Adapter Developer's Guide](https://github.com/istio/istio/blob/master/mixer/doc/dev/adapters.md) can help 
+you easily integrate your solution with Istio. 
 
 * _Bring your own CA certificates_: Allows users to provide their own key and certificate for Istio CA and persistent CA key/certificate Storage. Enables storing signing key/certificates in persistent storage to facilitate CA restarts.