The 'layout' of each page, that is, the top and bottom banners and the navigation bar, are determined by the JSPs /layout/header-*.jsp and /layout/footer-*.jsp. You can provide modified versions of these (in [jsp.custom-dir]/dspace/modules/jspui/src/main/webapp/layout), or define more styles and apply them to pages by using the "style" attribute of the dspace:layout tag.
The basic branding of the public pages of the repository is possible editing the header-default.jsp file and specifically the "container banner" div https://github.com/DSpace/DSpace/blob/dspace-6_x/dspace-jspui/src/main/webapp/layout/header-default.jsp#L133 this banner is shown in all the public page but hide in "backend functionalities" to allow more space for the functionality itself.
For the backend pages, both administrative than "registred user", you should edit the header-submission.jsp.
To change colors, fonts and CSS settings in general It is preferable to generate a new bootstrap.css using the tool provided by the bootstrap creator here: https://getbootstrap.com/docs/3.3/customize/ or choose one of the several themes available for bootstrap online, like the freely available provided by bootwatch
Rebuild the DSpace installation package by running the following command from your [dspace-source]/dspace/ directory:
Update all DSpace webapps to [dspace]/webapps by running the following command from your [dspace-source]/dspace/target/dspace-installer directory:
ant -Dconfig=[dspace]/config/dspace.cfg update
Deploy the the new webapps:
cp -R /[dspace]/webapps/* /[tomcat]/webapps
- Restart Tomcat
When you restart the web server you should see your customized JSPs.