As it has been discussed in answer 3357 (site: 3870) on our website, based on verse 21 of Surah of Al-Kahf ("قالَ الَّذينَ غَلَبُوا عَلى‏ أَمْرِهِمْ لَنَتَّخِذَنَّ عَلَيْهِمْ مَسْجِدا")[1] building a mosque near a grave and, by extension, offering prayers in it cannot be by itself an action against Islamic teachings and standards. However, the existing traditions in this regard can be assessed and analyzed into different sets:
First set: There are many traditions which not only allow worshipping near the graves of the noble servants of Allah but such a practice also earns the individual profuse reward.  There are so many such traditions from the Ahlul-Bayt (AS) that they leave no room for any opposition. For instance, there are at least ten narrations about offering prayers beside the grave of the Chief of Martyrs, Imam Hussein (AS). These narrations have been discussed in an independent chapter in Wasail al-Shi'ah.[2]
Second set: There are narrations such as those mentioned in your message which apparently signify prohibition or undesirability of building any structures or mosques over graves or establishing prayers beside them.
Keeping these two sets of traditions into consideration, we must say that due to the explicit verse of the Quran and the first set of traditions regarding permissibility of building any elevated structures on tombs, we must consider the second set of traditions as somehow dealing with respecting the graves, a practice which might lead to polytheism (shirk), extravagance, selfish pride and misuse of the characters of the dead etc. However, common respect and tribute paid to the graves of the noble servants of God that do not run counter to our servitude to the Lord and which is in line with servitude cannot be included in this prohibition.
In other words, the holy verse and the first category of narrations explain an established rule but the second category of narrations signify a transient rule which has been made incumbent due to the circumstance existing in that time.
Now, we shall explain some of the reasons which might have led to the issuance of the second category of narration. The explanation follows briefly as under:
1. Opposition to divine command:  At first glance, prostrating in front of the graves is not and cannot be polytheistic per se just as prayer and prostration in front of the  Ka'abah do not mean worshipping the Ka'abah. We can take the assumption that the prayer has been offered in front of some other symbols, but it had been for God. Another example is God's order to the angels to prostrate themselves before Prophet Adam (AS)[3] Also, there is another divine command in the Quran about offering prayers in front of the maqam (station) of Ibrahim (AS)[4] and we know for sure that the maqam is where Abrahim's foot trace is left and could be seen by pilgrims.  If building a structure, and offering prayers beside or in front of them are signs of servitude to God, we cannot, for instance, say that offering prayers beside or even in front of Ibrahim's grave in Palestine is a polytheistic act. However, since God has fixed the Qibla, we cannot arbitrarily consider another place as another Qibla even though it might be a sacred place.
It is likely that cursing the Jews and Christians on the part of the Holy Prophet (S) was, mainly, due to the fact that they stubbornly and intractably took their prophets' graves as their qibla. The Holy Prophet (S) were concerned that some might arbitrarily offer their prayers in the direction of his grave rather than to the divinely appointed qibla.
2. Rivalry and selfish pride:  By going through the interpretation of the Holy Qur'an[5], we come across an incident in which individuals from two different clans spoke very high of their leaders and  chieftains taking pride over them. When they were dead, they began speaking of the merits and attributes of their predecessors until the initial verses of Surah Takaturh were revealed. "أَلْهاكُمُ التَّكاثُر. حَتَّى زُرْتُمُ الْمَقابِر ..." The mutual rivalry (greediness) for piling up diverts you (from the more serious things), until you visited the graves (i.e. you enumerates of your dead ones and took pride over them.).
Naturally, such an approach to the dead, misusing their names and personalities as well as building extraordinary tombs on their graves to satisfy the carnal desires cannot be endorsed and accepted by Islam. Many traditions forbidding from building any kind of edifices on graves are possibly referring to such a conduct on the part of those people. Unfortunately, even today we also see some family graves with edifices on them.
3. Extravagance in normal lamentations: Despite the religion of Islam emphasizing patience and forbearance against inflicted calamities, we can see that some people go to extremes while mourning over the death of dear and near. Such people tend to disbelieve in the reward promised for those who exercise patience. Some of the narrations may imply that the death of our dear and near should not prevent us from living a dignified life.
4. The dead do no benefit from decorated graves:  Long time ago some people used to believe that the dead needed food, suitable place, jewelry etc. That is why traces of such decorations could be seen in old graves in ancient civilizations. Some of the traditions can also signify the fact that reconstructing graves with such an attitude is not appropriate and that material facility built beside the graves would be of no avail to the dead.
5.  Possibility of reversing to idolatry:  Due, largely, to the fact that in the early period of Islam, polytheistic mindset had not been obliterated from public mind, the probability of ignorant beliefs returning to Islamic society was threatening Muslims. That was why the Holy Prophet, peace be upon him and his family, adopted stricter measures about certain allowable things so as to help uproot shirk (polytheistic conducts). Naturally, after shirk was uprooted, stricter actions were required to be taken to keep the society healthy.
Among these actions by the Holy Prophet (S) was to break the containers in which wine used to be kept, even though we know that such an action is not obligatory for the time being.
Some of the Holy Prophet's strict measures in connection with graves can be evaluated in line with the same objective. For instance, Sunnis believe that the Prophet (S) also forbade Muslims from visiting graves but with the passage of time, not only was the ban lifted but he also advised them to visit graves as he announced visitation of graves to be a reminder of death, resurrection and would finally lead to piety in this world. [6] With that said and keeping in view of the existing realities with the Shia shrines, we can come to the conclusion that building any edifices around their graves is like building a mosque over the graves of the Companions of the Cave and a  place deemed to be for worshippers. The facilities existing around or near the shrines are meant for the convenience of the pilgrims or they are symbols of Islamic art and they are manifestations of negative things in connection with graves. Therefore, they cannot be considered as invalid and unacceptable from legal or religious perspective.  It is prudent to mention that a similar situation which is the demand of the moment can be seen with some holy sites in the Two Holy Sanctuaries with structures and edifices being made.  For instance:
1. Despite the fact that according to Shia and Sunni traditions, worshipping on  Mount Safa has a lot of reward, today a fence has been built around it to protect it and a also a tomb has been erected on top of it. The pilgrims of the House of Allah can stand only near the rails and engage in praying. Moreover, the ritual of Sa'y between Safa and Marwa which used to be performed on an open ground is now performed on different floors or levels with ceilings. The reason is the increasing number of pilgrims performing hajj rituals each year.
2. It is necessary to observe the respect and sanctity of Ka'aba under any circumstances to the extent that according to some narrations, building any structures or buildings higher than the Ka'aba is considered to be abominable (makrooh)[7] but today there are buildings, towers and skyscrapers many times higher than the Ka'abah. Certainly, the need of pilgrims of the House of Allah is the only justification presented in this regard.
Now our question is that is it not possible to create, under these justifications, accommodations and build a roofed facility for pilgrims who face a lot of difficulties while performing pilgrimage?  If building a tomb over Safa and Marwa mountains is not a sign of shirk (act of worshipping something other than the One God), how can the same tomb on top of the graves of the noble servants of God be a sign of shirk?
In closing, the reader is advised to take notice of narration cited from Sahih Bukhari. The narrator quotes Sufyan Tammar as saying, "I saw the grave of the Prophet (S) like a hump of camel (something like a small tomb)."[8]
When the population of Muslims was small and the graves had been built in such a way that they looked like small tombs, what would be the problem, if a bigger tomb is built in the present time when Muslim population has grown manifold?  

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