The subsidiary indication in each clue leads to an extra letter. These letters indicate the source of two questions (the second of which WAS rhetorical) and reveal a recent and unresolved problem (from which two of the unclued grid entries may be deduced).
The extra letters in the across clues gave ‘last lines of old vicarage’ which refers to Rupert Brooke’s poem “The Old Vicarage, Grantchester”. The last lines of this are:
“Stands the Church clock at ten to three?
And is there honey still for tea?”
Those in the down clues spelt out ‘colony collapse disorder’ which is the name of a problem affecting beekeepers where the worker bees disappear from a hive (see: http://en.wikipedia.org/wiki/Colony_collapse_disorder). This problem has increased in recent years.
The two unclued entries that could be deduced from the problem were COLONEL (14a) and CALYPSO (40a) because together they form an anagram (disorder) of COLONY COLLAPSE.
One meaning of a four-times absent word should enable solvers to address the first question by joining three cells appropriately.
In four answers (21a, 22a, 7d & 9d) the word BEE had to be omitted before grid entry (but this still left real words). One definition for ‘bee’ in Chambers is the letter ‘B’, three of which appear in the grid, one in the centre square, one at the end of 2d and one at the beginning of 28d. A straight line drawn from the central B to each of the other two gives clock hands which reveal that the time is indeed ten to three.
Solvers must also deduce a regrettably empty thematic word (4) and fill it thereby creating a sign of celebration and 4 new words.
Prior to this point, 44a was empty apart from the first and last letters. As these were H and E it was easy to see that the thematic word that needed to be filled was HIVE. The result had to be a sign of celebration so the only possible answer was HIGH-FIVE. Entering this formed new words at 25d, 30d, 34d and 36d.
A most enjoyable puzzle with a few twists towards the end and something new (colony collapse disorder) learnt along the way. It was interesting that Charybdis chose to link a classic poem with a modern phenomena. For me this added something to the puzzle.
*(XXX) – anagram
[x] – letters cut/unused
{s} – extra letters in wordplay
Across
1 ADSUM {l}AD (boy) SUM (problem)
5 TITHE-PIG *(IT HIT P{a}GE)
11 ROOF ROO (Antipodean jumper) {s}F (briefly forced)
12 HAHA HA{t}HA[way] (Shakespeare’s wife, no way)
13 MIRA [ad]MIRA{l} (navel officer misses advertisement)
14 COLONEL see preamble
15 ARENAS NA{i} (North American Institute) in ARES (war god)
16 ASSOIL ASS (donkey) LIO{n} (big cat) reversed
18 ECHIURA ECHIU[m] (viper’s bugloss) R{e}A[p] (harvest)
20 MORNE R (80) in *(MEN {s}O)
21 SEA{bee}S {o}BE (British order) in *(EASES)
22 WILDE{bee}ST WI (Women’s Institute) L (left) {f}ees (charges for services) in DEBT (what’s owed)
26 EMBAY {o}M (an order) in EBAY (on-line marketplace)
29 CLEANSE C (calorie) LEAN (low in fat) SE{l}[dom]
31 MEAT MEA{d} (honey drink) T (time)
33 ROADS R[oman] [qu]O {v}AD[i]S (Quo vadis? Qui va?) – ‘va’ = goes in French
35 DECLARE *(C{i}DER ALE)
37 NETHER NET (after tax deductions) {c}HER (dear)
39 NORIAS {a}S (like) A IRON (revolver) reversed
40 CALYPSO see preamble
41 CUES CU{r}ES (makes better)
42 REST RES{a}T (took the exam again)
43 LINN LIN{g} (heather) N (new)
44 HIGH-FIVE see preamble
45 WATTS W (women) ATT{e}S[t] (mostly aver)
Down
1 ARCHES ARCH (cunning) ES{c} (escape)
2 DOOB DO (first note) OB{o}[e] (shortened reed instrument)
3 SOLA HAT SOLA (cry from far away) HA{l}T (check further movement)
4 MENSUREN {o}MEN (threatening character) SURE (certainly) N (new)
5 THEOREM E[uclid] in THE {n}ORM (as a rule)
6 THALLI ALL{y} (help) in THI[s]
7 HARAM{bee} HA (this year) *(EMBRA{c}E)
8 EMERODS EME (old uncle) ROD (Rodney) {o}S (very big)
9 {bee}PING B (bachelor) [s]{l}EEPING (dozing out of sun)
10 GAS JETS JET (form of coal) in G{l}ASS (beaker)
17 ENSEAR *(SE{a}N) [d]EAR
19 CEYLON CE (church) {p}YLON (gateway)
23 LYNCH-LAW *(N{s} WHY CALL)
24 SCRUNCH S{e}C (dry) RUNCH (charlock)
25 CADDIS CAD (knave) D{d} (gave as a gift) IS (Iceland, IVR)
27 ACETATE ACE (outstanding) TAT{i} (French comic) E (energy)
28 BEAR PIT BEAR (suffer) {s}PIT (dig)
30 SENSE N{o}S (refusals) in SEE (understand)
32 TENONS N (note) in TENO{r}S (singers)
34 SCAR SC[orec]AR{d}
36 ARE A RE{e} (Scots enclosure)
38 ISNT SI{r} reversed NT (National Trust)
I found this puzzle enjoyable except for the completion of 44a). HIVE was fairly obvious, as explained above but I though that the addition of GHFI to make HIGH-FIVE was a bit arbitrary.
There is no other word fitting HI….VE.