Fix multiple quality issues in the source

This PR fixes multiple issues in the source code to address issues raised by
tests/scripts/check-files.py. Specifically:
 * incorrect file permissions
 * missing newline at the end of files
 * trailing whitespace
 * Tabs present
 * TODOs in the souce code
diff --git a/library/asn1write.c b/library/asn1write.c
index 69b61b2..9555eca 100644
--- a/library/asn1write.c
+++ b/library/asn1write.c
@@ -232,7 +232,6 @@
     int ret;
     size_t len = 0;
 
-    // TODO negative values and values larger than 128
     // DER format assumes 2s complement for numbers, so the leftmost bit
     // should be 0 for positive numbers and 1 for negative numbers.
     //
diff --git a/library/ecjpake.c b/library/ecjpake.c
index e8f4086..ec5a400 100644
--- a/library/ecjpake.c
+++ b/library/ecjpake.c
@@ -301,7 +301,7 @@
  */
 static int ecjpake_zkp_write( const mbedtls_md_info_t *md_info,
                               const mbedtls_ecp_group *grp,
-                              const int pf, 
+                              const int pf,
                               const mbedtls_ecp_point *G,
                               const mbedtls_mpi *x,
                               const mbedtls_ecp_point *X,
diff --git a/library/net_sockets.c b/library/net_sockets.c
index 345f102..a1128dc 100644
--- a/library/net_sockets.c
+++ b/library/net_sockets.c
@@ -271,7 +271,7 @@
 static int net_would_block( const mbedtls_net_context *ctx )
 {
     int err = errno;
-    
+
     /*
      * Never return 'WOULD BLOCK' on a non-blocking socket
      */
diff --git a/library/ssl_cli.c b/library/ssl_cli.c
index a7aaaff..15599c9 100644
--- a/library/ssl_cli.c
+++ b/library/ssl_cli.c
@@ -355,7 +355,7 @@
 
     *olen = 6;
 }
-#endif /* MBEDTLS_ECDH_C || MBEDTLS_ECDSA_C || 
+#endif /* MBEDTLS_ECDH_C || MBEDTLS_ECDSA_C ||
           MBEDTLS_KEY_EXCHANGE_ECJPAKE_ENABLED */
 
 #if defined(MBEDTLS_KEY_EXCHANGE_ECJPAKE_ENABLED)
@@ -1284,7 +1284,7 @@
                                     MBEDTLS_SSL_ALERT_MSG_HANDSHAKE_FAILURE );
     return( MBEDTLS_ERR_SSL_BAD_HS_SERVER_HELLO );
 }
-#endif /* MBEDTLS_ECDH_C || MBEDTLS_ECDSA_C || 
+#endif /* MBEDTLS_ECDH_C || MBEDTLS_ECDSA_C ||
           MBEDTLS_KEY_EXCHANGE_ECJPAKE_ENABLED */
 
 #if defined(MBEDTLS_KEY_EXCHANGE_ECJPAKE_ENABLED)
diff --git a/library/ssl_srv.c b/library/ssl_srv.c
index aca4235..e897ff4 100644
--- a/library/ssl_srv.c
+++ b/library/ssl_srv.c
@@ -793,7 +793,7 @@
     const mbedtls_ssl_ciphersuite_t *suite_info;
 
 #if defined(MBEDTLS_SSL_PROTO_TLS1_2) && \
-    defined(MBEDTLS_KEY_EXCHANGE__WITH_CERT__ENABLED)    
+    defined(MBEDTLS_KEY_EXCHANGE__WITH_CERT__ENABLED)
     mbedtls_pk_type_t sig_type;
 #endif
 
@@ -2961,7 +2961,7 @@
             return( ret );
         }
 
-#if defined(MBEDTLS_KEY_EXCHANGE__WITH_SERVER_SIGNATURE__ENABLED)        
+#if defined(MBEDTLS_KEY_EXCHANGE__WITH_SERVER_SIGNATURE__ENABLED)
         dig_signed = p;
         dig_signed_len = len;
 #endif
@@ -3050,7 +3050,7 @@
 
         /*
          * 3.1: Choose hash algorithm:
-         * A: For TLS 1.2, obey signature-hash-algorithm extension 
+         * A: For TLS 1.2, obey signature-hash-algorithm extension
          *    to choose appropriate hash.
          * B: For SSL3, TLS1.0, TLS1.1 and ECDHE_ECDSA, use SHA1
          *    (RFC 4492, Sec. 5.4)
@@ -3071,7 +3071,7 @@
                                                           sig_alg ) ) == MBEDTLS_MD_NONE )
             {
                 MBEDTLS_SSL_DEBUG_MSG( 1, ( "should never happen" ) );
-                /* (... because we choose a cipher suite 
+                /* (... because we choose a cipher suite
                  *      only if there is a matching hash.) */
                 return( MBEDTLS_ERR_SSL_INTERNAL_ERROR );
             }
diff --git a/library/ssl_tls.c b/library/ssl_tls.c
index 8db46c3..6d7ad33 100644
--- a/library/ssl_tls.c
+++ b/library/ssl_tls.c
@@ -6916,41 +6916,6 @@
         }
     }
 
-    /*
-     * TODO
-     *
-     * The logic should be streamlined here:
-     *
-     * Instead of
-     *
-     * - Manually checking whether ssl->in_offt is NULL
-     * - Fetching a new record if yes
-     * - Setting ssl->in_offt if one finds an application record
-     * - Resetting keep_current_message after handling the application data
-     *
-     * one should
-     *
-     * - Adapt read_record to set ssl->in_offt automatically
-     *   when a new application data record is processed.
-     * - Always call mbedtls_ssl_read_record here.
-     *
-     * This way, the logic of ssl_read would be much clearer:
-     *
-     * (1) Always call record layer and see what kind of record is on
-     *     and have it ready for consumption (in particular, in_offt
-     *     properly set for application data records).
-     * (2) If it's application data (either freshly fetched
-     *     or something already being partially processed),
-     *     serve the read request from it.
-     * (3) If it's something different from application data,
-     *     handle it accordingly, e.g. potentially start a
-     *     renegotiation.
-     *
-     * This will also remove the need to manually reset
-     * ssl->keep_current_message = 0 below.
-     *
-     */
-
     if( ssl->in_offt == NULL )
     {
         /* Start timer if not already running */