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How do I fix SEVERE: Allocate exception for servlet after Project clean?

I am working on a dynamic web project using JSP and multiple servlets with tomcat Apache and Eclipse.
I was having multiple problems with Eclipse today and I ran a clean on the project to try to fix some of the issues that I was having and ever since, I'm getting the following error every time a servlet is called.
SEVERE: Allocate exception for servlet [RegisterServlet]
java.lang.ClassNotFoundException: com.ogi.controller.RegisterServlet
at org.apache.catalina.loader.WebappClassLoaderBase.loadClass(WebappClassLoaderBase.java:1372)
at org.apache.catalina.loader.WebappClassLoaderBase.loadClass(WebappClassLoaderBase.java:1195)
at org.apache.catalina.core.DefaultInstanceManager.loadClass(DefaultInstanceManager.java:545)
at org.apache.catalina.core.DefaultInstanceManager.loadClassMaybePrivileged(DefaultInstanceManager.java:526)
at org.apache.catalina.core.DefaultInstanceManager.newInstance(DefaultInstanceManager.java:150)
at org.apache.catalina.core.StandardWrapper.loadServlet(StandardWrapper.java:1044)
at org.apache.catalina.core.StandardWrapper.allocate(StandardWrapper.java:763)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:134)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:97)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:544)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:143)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:81)
at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:698)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:78)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:353)
at org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:616)
at org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:65)
at org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:831)
at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1629)
at org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:49)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
at java.base/java.lang.Thread.run(Thread.java:830)
This project was working completely fine on localhost before the clean and I have all of the servlets defined in my web.xml file. CATALINA has an environmental variable and I already have the Jar files in my project.
I'm not sure why these errors are occurring and would appreciate some direction on how to attempt to fix this.

Tomcat can't find Log4j library

I'm trying to deploy a .war using Tomcat 8.5.56 (I have to use this version for company policy), it logs with Log4j and it is all setted at WEB-INF/web.xml as you can see here:
...
<env-entry>
<env-entry-name>LogClassName</env-entry-name>
<env-entry-value>com.lutris.logging.Log4jLogger</env-entry-value>
<env-entry-type>java.lang.String</env-entry-type>
</env-entry>
<env-entry>
<env-entry-name>Log4j</env-entry-name>
<env-entry-value>../conf/log4j.xml</env-entry-value>
<env-entry-type>java.lang.String</env-entry-type>
</env-entry>
...
When I search the application url, I got a 500 Server error with the next message:
javax.servlet.ServletException: Initialization of logger failed
caused by class com.lutris.util.ConfigException: Key "LogFile" not found in configuration.
com.lutris.appserver.server.httpPresentation.servlet.HttpPresentationServlet.throwServletException(Unknown Source)
com.lutris.appserver.server.httpPresentation.servlet.HttpPresentationServlet.init(Unknown Source)
org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:543)
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:81)
org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:690)
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:343)
org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:615)
org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:65)
org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:818)
org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1627)
org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:49)
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
java.lang.Thread.run(Thread.java:748)
After a long search I found that this problem comes up because it cant't find the LogClassName class and try to use the default logger, but all the .jars files are at the lib path in tomcat_folder/lib. At first I thought it would be solved if I put that .jars at the app lib folder (tomcat_folder/webapps/application/WEB-INF/lib) but the problem is still there.
Any help would be greatly appreciated.

Tomcat server not working anymore after a stop and restart

I've got an error related to tomcat server. I shut down my server (took a while) and then when a start the server back, an error appears :
org.springframework.jmx.export.UnableToRegisterMBeanException: Unable to register MBean [com.amadeus.security.CCDVAccess#2a9cce4a] with key 'CCDVAccess'; nested exception is javax.management.InstanceAlreadyExistsException: com.amadeus.security:name=CCDVAccess
org.springframework.jmx.export.MBeanExporter.registerBeanNameOrInstance(MBeanExporter.java:625)
org.springframework.jmx.export.MBeanExporter.registerBeans(MBeanExporter.java:550)
org.springframework.jmx.export.MBeanExporter.afterSingletonsInstantiated(MBeanExporter.java:432)
org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:795)
org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:861)
org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:541)
org.springframework.web.servlet.FrameworkServlet.configureAndRefreshWebApplicationContext(FrameworkServlet.java:668)
org.springframework.web.servlet.FrameworkServlet.createWebApplicationContext(FrameworkServlet.java:634)
org.springframework.web.servlet.FrameworkServlet.createWebApplicationContext(FrameworkServlet.java:682)
org.springframework.web.servlet.FrameworkServlet.initWebApplicationContext(FrameworkServlet.java:553)
org.springframework.web.servlet.FrameworkServlet.initServletBean(FrameworkServlet.java:494)
org.springframework.web.servlet.HttpServletBean.init(HttpServletBean.java:136)
javax.servlet.GenericServlet.init(GenericServlet.java:158)
org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:632)
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:79)
org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:620)
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:349)
org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:1110)
org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:66)
org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:785)
org.apache.tomcat.util.net.Nio2Endpoint$SocketProcessor.doRun(Nio2Endpoint.java:1627)
org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:49)
org.apache.tomcat.util.net.AbstractEndpoint.processSocket(AbstractEndpoint.java:830)
org.apache.tomcat.util.net.Nio2Endpoint$Nio2SocketWrapper$4.completed(Nio2Endpoint.java:639)
org.apache.tomcat.util.net.Nio2Endpoint$Nio2SocketWrapper$4.completed(Nio2Endpoint.java:617)
org.apache.tomcat.util.net.SecureNio2Channel$1.completed(SecureNio2Channel.java:873)
org.apache.tomcat.util.net.SecureNio2Channel$1.completed(SecureNio2Channel.java:806)
sun.nio.ch.Invoker.invokeUnchecked(Invoker.java:126)
sun.nio.ch.Invoker$2.run(Invoker.java:218)
sun.nio.ch.AsynchronousChannelGroupImpl$1.run(AsynchronousChannelGroupImpl.java:112)
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
java.lang.Thread.run(Thread.java:745)
I know that the error is not related to the code, because nothing change.
I try
to stop and restart many times,
to change the version of the WAR I was using.
to delete the logs and the folder work/catalina
I do not know what else I should try, so I hope some of you has I idea about that. I really think the issue is coming from tomcat but I'm not sure.
Thank for your help
Sébastien
Edit: I solved my issue it was a stupid mistake. I did a backup of my WAR file without changing the extension... Therefore tomcat was launching 2 identicals servers.
Thanks guys for your help

it seems you have two Spring Boot apps in the same JVM so you need to segregate the MBean namespace.
the first log error tell you that.
org.springframework.jmx.export.UnableToRegisterMBeanException: Unable
to register MBean [com.amadeus.security.CCDVAccess#2a9cce4a] with key
'CCDVAccess'; nested exception is
javax.management.InstanceAlreadyExistsException:
com.amadeus.security:name=CCDVAccess
for further clarification
https://github.com/spring-cloud/spring-cloud-config/issues/118.

javax.xml.validation.SchemaFactoryConfigurationError: Provider for class javax.xml.validation.SchemaFactory cannot be created

Got below exceptions, when I tried to run my web application using tomcat(on server start up).[upgraded java 7 to java 8 and tomcat 7 to 8.5]
Jar used: xercesImpl-2.11.0.jar
SEVERE: Critical error during deployment:
javax.xml.validation.SchemaFactoryConfigurationError: Provider for class javax.xml.validation.SchemaFactory cannot be created
at javax.xml.validation.SchemaFactoryFinder.findServiceProvider(SchemaFactoryFinder.java:414)
at javax.xml.validation.SchemaFactoryFinder._newFactory(SchemaFactoryFinder.java:218)
at javax.xml.validation.SchemaFactoryFinder.newFactory(SchemaFactoryFinder.java:145)
at javax.xml.validation.SchemaFactory.newInstance(SchemaFactory.java:213)
at com.sun.faces.util.Util.createSchemaFactory(Util.java:237)
at com.sun.faces.config.DbfFactory.initStatics(DbfFactory.java:247)
at com.sun.faces.config.DbfFactory.(DbfFactory.java:209)
at com.sun.faces.config.ConfigManager$ParseTask.(ConfigManager.java:892)
at config.ConfigManager.getConfigDocuments(ConfigManager.java:652)
at nfig.ConfigManager.initialize(ConfigManager.java:324)
at ConfigureListener.contextInitialized(ConfigureListener.java:223)
at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4745)
org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5207)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:752)
at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:728)
at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:734)
at org.apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java:630)
at org.apache.catalina.startup.HostConfig$DeployDescriptor.run(HostConfig.java:1842)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)
Caused by: java.util.ServiceConfigurationError: javax.xml.validation.SchemaFactory: jar:file:/C:/Program%20Files/Apache%20Software%20Foundation/Tomcat8.5/lib/wlfullclient.jar!/META-INF/services/javax.xml.validation.SchemaFactory:1: Illegal provider-class name: http://www.w3.org/2001/XMLSchema=org.apache.xerces.jaxp.validation.XMLSchemaFactory
at java.util.ServiceLoader.fail(ServiceLoader.java:239)
at java.util.ServiceLoader.fail(ServiceLoader.java:245)
at java.util.ServiceLoader.parseLine(ServiceLoader.java:272)
at java.util.ServiceLoader.parse(ServiceLoader.java:307)
at java.util.ServiceLoader.access$200(ServiceLoader.java:185)
at java.util.ServiceLoader$LazyIterator.hasNextService(ServiceLoader.java:357)
at java.util.ServiceLoader$LazyIterator.hasNext(ServiceLoader.java:393)
at java.util.ServiceLoader$1.hasNext(ServiceLoader.java:474)
at javax.xml.validation.SchemaFactoryFinder$2.run(SchemaFactoryFinder.java:403)
at javax.xml.validation.SchemaFactoryFinder$2.run(SchemaFactoryFinder.java:399)
at java.security.AccessController.doPrivileged(Native Method)
at

Took wlfullclient.jar from my QA server and placed same in local upgraded tomcat.
When I compared I found QA's wlfullclient.jar size was much bigger than what I had in my local tomcat. Then I thought lets try it out with this. and that worked.
Thanks

Tesseract - ERROR net.sourceforge.tess4j.Tesseract - null

Created a java application that uses Tesseract in order to convert a given image or pdf to a string format, when running it on my machine as a unit test using junit it runs great but when running the full system which is a restFul API run by tomcat that receives the image and runs Tesseract it gives me the following error:
23:22:36.511 [http-nio-9999-exec-3] ERROR
net.sourceforge.tess4j.Tesseract - null
java.lang.NullPointerException: null at
net.sourceforge.tess4j.util.PdfUtilities.convertPdf2Png(PdfUtilities.java:107)
at
net.sourceforge.tess4j.util.PdfUtilities.convertPdf2Tiff(PdfUtilities.java:48)
at
net.sourceforge.tess4j.util.ImageIOHelper.getIIOImageList(ImageIOHelper.java:343)
at net.sourceforge.tess4j.Tesseract.doOCR(Tesseract.java:213) at
net.sourceforge.tess4j.Tesseract.doOCR(Tesseract.java:197) at
ocr.OcrUtil.getString(OcrUtil.java:54) at
com.tapd.server.api.handlers.IRSHandler.uploadIRSImage(IRSHandler.java:65)
at
com.tapd.server.api.WebAPIService.updateParentIrsForm(WebAPIService.java:250)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at
sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source) at
sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source) at
java.lang.reflect.Method.invoke(Unknown Source) at
org.glassfish.jersey.server.model.internal.ResourceMethodInvocationHandlerFactory$1.invoke(ResourceMethodInvocationHandlerFactory.java:81)
at
org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher$1.run(AbstractJavaResourceMethodDispatcher.java:144)
at
org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher.invoke(AbstractJavaResourceMethodDispatcher.java:161)
at
org.glassfish.jersey.server.model.internal.JavaResourceMethodDispatcherProvider$ResponseOutInvoker.doDispatch(JavaResourceMethodDispatcherProvider.java:160)
at
org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher.dispatch(AbstractJavaResourceMethodDispatcher.java:99)
at
org.glassfish.jersey.server.model.ResourceMethodInvoker.invoke(ResourceMethodInvoker.java:389)
at
org.glassfish.jersey.server.model.ResourceMethodInvoker.apply(ResourceMethodInvoker.java:347)
at
org.glassfish.jersey.server.model.ResourceMethodInvoker.apply(ResourceMethodInvoker.java:102)
at
org.glassfish.jersey.server.ServerRuntime$2.run(ServerRuntime.java:309)
at org.glassfish.jersey.internal.Errors$1.call(Errors.java:271) at
org.glassfish.jersey.internal.Errors$1.call(Errors.java:267) at
org.glassfish.jersey.internal.Errors.process(Errors.java:315) at
org.glassfish.jersey.internal.Errors.process(Errors.java:297) at
org.glassfish.jersey.internal.Errors.process(Errors.java:267) at
org.glassfish.jersey.process.internal.RequestScope.runInScope(RequestScope.java:317)
at
org.glassfish.jersey.server.ServerRuntime.process(ServerRuntime.java:292)
at
org.glassfish.jersey.server.ApplicationHandler.handle(ApplicationHandler.java:1139)
at
org.glassfish.jersey.servlet.WebComponent.service(WebComponent.java:460)
at
org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:386)
at
org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:334)
at
org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:221)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:230)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:165)
at
org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:192)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:165)
at
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:198)
at
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:108)
at
org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:522)
at
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:140)
at
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:79)
at
org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:620)
at
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:87)
at
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:349)
at
org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:1110)
at
org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:66)
at
org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:785)
at
org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1425)
at
org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:49)
at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at
org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
at java.lang.Thread.run(Unknown Source) [2016-09-14 23:22:36,512]
[ERROR] java.lang.NullPointerException
My guess is that the tessdata folder is not located in the right place and when packaged into a Jar and run by tomcat it is misplaced, but I couldn't figure out where it should be located and I have double checked to see that all Jars are deployed correctly.
Edit: so it appears that Tesseract can't handle the path when it is on a remote server such as AWS S3, so the question is why? and how can I allow it to use a path from S3? (yes the file is public)

My guess is that there is GhostscriptException which is not logged properly, and this is causing NullPointerException:
https://github.com/nguyenq/tess4j/blob/212d72bc2ec8b3a4d4f5a18f1eb01a0622fc5521/src/main/java/net/sourceforge/tess4j/util/PdfUtilities.java#L107
106 } catch (GhostscriptException e) {
107 logger.error(e.getCause().toString(), e);
108 } finally {
In line 107 - e.getCause() is (probably) null, calling null.toString() throws NPE.
(from the specs - getCause can be null:
https://docs.oracle.com/javase/7/docs/api/java/lang/Throwable.html#getCause(), GhostscriptException is also allowing the cause to be null: http://grepcode.com/file/repo1.maven.org/maven2/org.ghost4j/ghost4j/1.0.0/org/ghost4j/GhostscriptException.java)
To verify this answer (without recompiling the whole tess4j) you could start your program in the debug mode and put a breakpoint at line 107. This will give you information about the real Exception.

As #Piotr R mentioned the error was ghostscriptException.getCause() is null and the reason for that is that the path configured in the file object sent to Tesseract was not a valid one, now the definition of valid for Tesseract is a bit different then yours, he consider only a local address as valid, so when setting a file located on AWS S3 even if it's public it will throw an error.
The solution was saving it locally and deleting it after Tesseract is done.

Resources I used: Windows 10 (tried on Windows Server 2016 as well), JAVA, MAVEN
Status: Working good on my local as well as VM
Download Tess4J-3.4.8 from here http://tess4j.sourceforge.net/ and set your ENV variable path under Advance System Setting
Get repo from MAVEN -
<dependency>
<groupId>net.sourceforge.tess4j</groupId>
<artifactId>tess4j</artifactId>
<version>4.5.1</version>
</dependency>
<dependency>
<groupId>org.ghost4j</groupId>
<artifactId>ghost4j</artifactId>
<version>1.0.1</version>
</dependency>
<dependency>
<groupId>net.sourceforge.lept4j</groupId>
<artifactId>lept4j</artifactId>
<version>1.7.0</version>
</dependency>
Get libtesseract302.dll and copy to "C:\Windows\System32" folder
from here http://api.256file.com/libtesseract302.dll/en-download-56466.html
do not forget to set your ENV variable path under Advance System Setting
Download and install Visual C++ 2015 Redistributable or VC++ 2017 Redistributable (I installed both )
from here https://programmer.help/blogs/net.sourceforge.tess4j.tesseractexception-java.lang.nullpointerexception.html
then do restart your PC
on Safer side can have some Jar files if you dont have already in local - Please see image
do not forget to set your ENV variable path for JARs under Advance System Setting