My tomcat logs are not showing any errors and from what I can tell the project is configured correctly as well as tomcat 9.
<properties>
        <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
        <java.version>1.8</java.version>
        <tomcat.version>9.0.0.M4</tomcat.version>
        <main.basedir>${basedir}/../..</main.basedir>
    </properties>
More for tomcat:
<!-- Provided (for embedded war support) -->
        <dependency>
            <groupId>org.springframework.boot</groupId>
            <artifactId>spring-boot-starter-tomcat</artifactId>
            <scope>provided</scope>
        </dependency>
        <dependency>
            <groupId>org.apache.tomcat.embed</groupId>
            <artifactId>tomcat-embed-core</artifactId>
            <version>${tomcat.version}</version>
        </dependency>
        <dependency>
            <groupId>org.apache.tomcat.embed</groupId>
            <artifactId>tomcat-embed-el</artifactId>
            <version>${tomcat.version}</version>
        </dependency>
        <dependency>
            <groupId>org.apache.tomcat.embed</groupId>
            <artifactId>tomcat-embed-logging-juli</artifactId>
            <version>${tomcat.version}</version>
        </dependency>
        <dependency>
            <groupId>org.apache.tomcat.embed</groupId>
            <artifactId>tomcat-embed-jasper</artifactId>
            <version>${tomcat.version}</version>
        </dependency>
        <dependency>
            <groupId>org.apache.tomcat.embed</groupId>
            <artifactId>tomcat-embed-websocket</artifactId>
            <version>${tomcat.version}</version>
        </dependency>
        <dependency>
            <groupId>org.apache.tomcat</groupId>
            <artifactId>tomcat-jdbc</artifactId>
            <version>${tomcat.version}</version>
        </dependency>
        <dependency>
            <groupId>org.apache.tomcat</groupId>
            <artifactId>tomcat-jsp-api</artifactId>
            <version>${tomcat.version}</version>
        </dependency>
        <dependency>
            <groupId>org.springframework.boot</groupId>
            <artifactId>spring-boot-starter-test</artifactId>
            <scope>test</scope>
        </dependency>
    </dependencies>
Also the index.jsp page renders but displays a blank page. I am using AngularJS and <ng-view> in the page. This is where I am getting the errors:
This is what is being loaded:
It is just loading some stylesheets and my index page.
I map the pages in the project like so:
@Configuration
public class WebConfig extends WebMvcConfigurerAdapter {
    private static final Logger LOGGER = Logger.getLogger(WebConfig.class);
    public void addResourceHandlers(ResourceHandlerRegistry registry) {
        registry.setOrder(Ordered.HIGHEST_PRECEDENCE);
        registry
            .addResourceHandler("/javascripts/**")
            .addResourceLocations("/resources/javascripts/");
        registry
            .addResourceHandler("/libs/**")
            .addResourceLocations("/resources/libs/");
        registry
            .addResourceHandler("/stylesheets/img/**")
            .addResourceLocations("/resources/images/");
        registry
            .addResourceHandler("/stylesheets/**")
            .addResourceLocations("/resources/stylesheets/");
        registry
            .addResourceHandler("/images/**")
            .addResourceLocations("/resources/images/");
        registry
            .addResourceHandler("/views/**", "/templates/**")
            .addResourceLocations("/resources/templates/");
    };
application.properties
spring.mvc.view.prefix=/WEB-INF/
spring.mvc.view.suffix=.jsp
spring.mvc.static-path-pattern=/resources/*
server.contextPath=/
map the index.jsp here:
@Controller
public class ApplicationController {
    @RequestMapping(value = {"/**", "*" }, method = RequestMethod.GET)
    public String index() {
        return "index";
    }
}
Once it hits the index.jsp file Angular routes should take over:
app.config(function($routeProvider, $locationProvider){
    $routeProvider.when('/',{
        templateUrl: "/templates/misc/home.tpl.html",
        controller: "HomeController"
    })
    .when('/features/blog',{
        templateUrl: "/templates/features/blog.tpl.html",
        controller: "BlogController"
    })
    .when('/features/blogpost',{
        templateUrl: "/templates/features/blog-post.tpl.html",
        controller: "BlogPostController"
    })
    .when('/features/portfolio',{
        templateUrl: "/templates/features/portfolio.tpl.html",
        controller: "PortfolioController"
    })
index.jsp
<body>
        <ng-include src="'/templates/structure/navigation.tpl.html'"></ng-include>
        This is just a test...
        <ng-view autoscroll="true"></ng-view>
        <ng-include src="'/templates/structure/footer.tpl.html'"></ng-include >
        <!--Scripts-->
        <!--<script src="bower_components/masonry/dist/masonry.pkgd.min.js"></script>-->
        <script src="http://ajax.googleapis.com/ajax/libs/jquery/2.1.1/jquery.min.js"></script>
        <script src="/libs/flexslider/jquery.flexslider.js"></script>
        <script src="/libs/masonry/masonry.pkgd.min.js"></script>
        <script src="/libs/imagesloaded/imagesloaded.pkgd.min.js"></script>
        <script src="/libs/angular/angular.min.js"></script>
        <script src="/libs/angular/angular-route.min.js"></script>
        <script src="/libs/angular/angular-sanitize.min.js"></script>
        <script src="/libs/angular/ui-bootstrap-tpls-0.13.0.min.js"></script>
        <script src="/libs/angular-flexslider/angular-flexslider.js"></script>
        <script src="/libs/angular-backstretch/ng-backstretch.min.js"></script>
        <script src="/libs/angular-parallax/angular-parallax.js"></script>
        <script src="/libs/angular-fitvids/angular-fitvids.js"></script>
        <script src="/libs/angular-masonry/angular-masonry.min.js"></script>
        <script src="/libs/momentjs/moment-with-locales.min.js"></script>
        <script src="/libs/humanize-duration/humanize-duration.js"></script>
        <script src="/libs/angular-timer/angular-timer.min.js"></script>
        <script src="/libs/ng-progress/js/ngprogress.min.js"></script>
        <script src="/libs/angular-gmaps/angular-google-maps.min.js"></script>
        <script src="/libs/lodash/lodash.min.js"></script>
        <script src='//maps.googleapis.com/maps/api/js?sensor=false'></script>
        <script src="/javascripts/app.module.js"></script>
        <script src="/javascripts/app.directives.js"></script>
        <script src="/javascripts/app.routes.js"></script>
        <script src="/javascripts/app.controllers.js"></script>
        <script src="/javascripts/app.service.js"></script>
    </body>
</html>
On the blank page it does render "This is just a test" but I get a 404 error for all my Angular and other dependencies, some of which can be seen on the first picture I posted.
My Directory:
------------------- Update 1------------------
context.xml
!-- The contents of this file will be loaded for each web application -->
<Context>
    <!-- Default set of monitored resources. If one of these changes, the    -->
    <!-- web application will be reloaded.                                   -->
    <WatchedResource>WEB-INF/web.xml</WatchedResource>
    <WatchedResource>${catalina.base}/conf/web.xml</WatchedResource>
    <!-- Uncomment this to disable session persistence across Tomcat restarts -->
    <!--
    <Manager pathname="" />
    -->
</Context>
--------------------Update 2-------------------
I had to add some JSTL tags and was then able to load the scripts. However now something really odd is happening:
<ng-include src="<c:url value="'/templates/structure/navigation.tpl.html'" />"></ng-include>
        <ng-view autoscroll="true"></ng-view>
        <ng-include src="<c:url value="'/templates/structure/footer.tpl.html'" />" ></ng-include>
All the above are showing 404 errors in the console and it renders a blank page.



 
    