How to design a good JWT authentication filter

Here is a filter that can do what you need :

public class JWTFilter extends GenericFilterBean {

    private static final Logger LOGGER = LoggerFactory.getLogger(JWTFilter.class);

    private final TokenProvider tokenProvider;

    public JWTFilter(TokenProvider tokenProvider) {

        this.tokenProvider = tokenProvider;
    }

    @Override
    public void doFilter(ServletRequest servletRequest, ServletResponse servletResponse, FilterChain filterChain) throws IOException,
        ServletException {

        try {
            HttpServletRequest httpServletRequest = (HttpServletRequest) servletRequest;
            String jwt = this.resolveToken(httpServletRequest);
            if (StringUtils.hasText(jwt)) {
                if (this.tokenProvider.validateToken(jwt)) {
                    Authentication authentication = this.tokenProvider.getAuthentication(jwt);
                    SecurityContextHolder.getContext().setAuthentication(authentication);
                }
            }
            filterChain.doFilter(servletRequest, servletResponse);

            this.resetAuthenticationAfterRequest();
        } catch (ExpiredJwtException eje) {
            LOGGER.info("Security exception for user {} - {}", eje.getClaims().getSubject(), eje.getMessage());
            ((HttpServletResponse) servletResponse).setStatus(HttpServletResponse.SC_UNAUTHORIZED);
            LOGGER.debug("Exception " + eje.getMessage(), eje);
        }
    }

    private void resetAuthenticationAfterRequest() {
        SecurityContextHolder.getContext().setAuthentication(null);
    }

    private String resolveToken(HttpServletRequest request) {

        String bearerToken = request.getHeader(SecurityConfiguration.AUTHORIZATION_HEADER);
        if (StringUtils.hasText(bearerToken) && bearerToken.startsWith("Bearer ")) {
            String jwt = bearerToken.substring(7, bearerToken.length());
            return jwt;
        }
        return null;
    }
}

And the inclusion of the filter in the filter chain :

public class SecurityConfiguration extends WebSecurityConfigurerAdapter {

    public final static String AUTHORIZATION_HEADER = "Authorization";

    @Autowired
    private TokenProvider tokenProvider;

    @Autowired
    private AuthenticationProvider authenticationProvider;

    @Override
    protected void configure(AuthenticationManagerBuilder auth) throws Exception {
        auth.authenticationProvider(this.authenticationProvider);
    }

    @Override
    protected void configure(HttpSecurity http) throws Exception {

        JWTFilter customFilter = new JWTFilter(this.tokenProvider);
        http.addFilterBefore(customFilter, UsernamePasswordAuthenticationFilter.class);

        // @formatter:off
        http.authorizeRequests().antMatchers("/css/**").permitAll()
        .antMatchers("/images/**").permitAll()
        .antMatchers("/js/**").permitAll()
        .antMatchers("/authenticate").permitAll()
        .anyRequest().fullyAuthenticated()
        .and().formLogin().loginPage("/login").failureUrl("/login?error").permitAll()
        .and().logout().permitAll();
        // @formatter:on
        http.csrf().disable();

    }
}

The TokenProvider class :

public class TokenProvider {

    private static final Logger LOGGER = LoggerFactory.getLogger(TokenProvider.class);

    private static final String AUTHORITIES_KEY = "auth";

    @Value("${spring.security.authentication.jwt.validity}")
    private long tokenValidityInMilliSeconds;

    @Value("${spring.security.authentication.jwt.secret}")
    private String secretKey;

    public String createToken(Authentication authentication) {

        String authorities = authentication.getAuthorities().stream().map(authority -> authority.getAuthority()).collect(Collectors.joining(","));

        ZonedDateTime now = ZonedDateTime.now();
        ZonedDateTime expirationDateTime = now.plus(this.tokenValidityInMilliSeconds, ChronoUnit.MILLIS);

        Date issueDate = Date.from(now.toInstant());
        Date expirationDate = Date.from(expirationDateTime.toInstant());

        return Jwts.builder().setSubject(authentication.getName()).claim(AUTHORITIES_KEY, authorities)
                    .signWith(SignatureAlgorithm.HS512, this.secretKey).setIssuedAt(issueDate).setExpiration(expirationDate).compact();
    }

    public Authentication getAuthentication(String token) {

        Claims claims = Jwts.parser().setSigningKey(this.secretKey).parseClaimsJws(token).getBody();

        Collection<? extends GrantedAuthority> authorities = Arrays.asList(claims.get(AUTHORITIES_KEY).toString().split(",")).stream()
                    .map(authority -> new SimpleGrantedAuthority(authority)).collect(Collectors.toList());

        User principal = new User(claims.getSubject(), "", authorities);

        return new UsernamePasswordAuthenticationToken(principal, "", authorities);
    }

    public boolean validateToken(String authToken) {

        try {
            Jwts.parser().setSigningKey(this.secretKey).parseClaimsJws(authToken);
            return true;
        } catch (SignatureException e) {
            LOGGER.info("Invalid JWT signature: " + e.getMessage());
            LOGGER.debug("Exception " + e.getMessage(), e);
            return false;
        }
    }
}

Now to answer your questions :

1. Done in this filter
2. Protect your HTTP request, use HTTPS
3. Just permit all on the /login URI (/authenticate in my code)