doxygen: Tidy up comments and add in missing modules

Make documentation more consistent across doxygen output.

Add in caching module.
Add in encoding/decoding module.
Add in application i/o internal module.

Move deprecated items out of respective modules.

include/coap2/encode.h

@@ -45,6 +45,12 @@ extern int coap_flsll(long long i);
 #define COAP_PSEUDOFP_ENCODE_8_4_DOWN(v,ls) (v < HIBIT ? v : (ls = coap_fls(v) - Nn, (v >> ls) & MMASK) + ls)
 #define COAP_PSEUDOFP_ENCODE_8_4_UP(v,ls,s) (v < HIBIT ? v : (ls = coap_fls(v) - Nn, (s = (((v + ((1<<ENCODE_HEADER_SIZE<<ls)-1)) >> ls) & MMASK)), s == 0 ? HIBIT + ls + 1 : s + ls))
 
+/**
+ * @defgroup encode Encode / Decode API
+ * API functions for endoding/decoding CoAP options.
+ * @{
+ */
+
 /**
  * Decodes multiple-length byte sequences. @p buf points to an input byte
  * sequence of length @p length. Returns the up to 4 byte decoded value.
@@ -99,6 +105,8 @@ unsigned int coap_encode_var_safe8(uint8_t *buf,
                                   size_t length,
                                   uint64_t value);
 
+/** @} */
+
 /**
  * @deprecated Use coap_encode_var_safe() instead.
  * Provided for backward compatibility.  As @p value has a