DOCUMENTATION: Better npm run doc, plus minor folder reorganization (#693)

src/Documentation/doc/advanced/bitnodes.md

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+# BitNodes
+
+A BitNode is an important part of the game's storyline.
+In the game, you discover what BitNodes are by following the trail of clues left by the mysterious `jump3r`.
+
+## What is a BitNode
+
+A BitNode is the complex simulated reality in which you reside.
+By following the messages from `jump3r`, you discover that humanity was enslaved by an advanced alien race, called the Enders, using virtual simulations that trapped the minds of humans.
+
+However, the Enders didn't just create a single virtual reality to enslave humans, but many different simulations.
+In other words, there are many different BitNodes that exist.
+These BitNodes are very different from each other.
+
+jump3r tells you that the only hope for humanity is to destroy all of these BitNodes.
+Therefore, the end goal for the player is to enter and then destroy each BitNode.
+
+Destroying a BitNode resets most of the player's progress but grants the player a powerful second-tier persistent upgrade called a [Source-File](sourcefiles.md).
+Different BitNodes grant different [Source-Files](sourcefiles.md).
+
+Each BitNode has unique characteristics that are related to varying backstories.
+For example, in one BitNode the world is in the middle of a financial catastrophe with a collapsing market.
+In this BitNode, most forms of income such as working at a [Company](../basic/companies.md) or [Hacknet Nodes](../basic/hacknet_nodes.md) are significantly less profitable.
+[Servers](../basic/servers.md) have less money on them and lowered growth rates, but it is easier to lower their security level using the `weaken` function.
+
+Furthermore, some BitNodes introduce new content and mechanics.
+For example, there is one BitNode that grants access to the [Singularity API](https://github.com/bitburner-official/bitburner-src/blob/dev/markdown/bitburner.singularity.md).
+There is another BitNode in which you can manage a [Gang](gang.md) to earn money and [Reputation](../basic/reputation.md).
+
+## How to destroy a BitNode
+
+Initially, the only way to destroy a BitNode is to join Daedalus.
+From Daedalus, the player can obtain an [Augmentation](../basic/augmentations.md) called `The Red Pill`, which doesn't cost any money but does require a good amount of [Faction](../basic/factions.md) [Reputation](../basic/reputation.md).
+
+After installing `The Red Pill`, the player must search for and then manually `hack` a server called `w0r1d_d43m0n`.
+This server requires a hacking level of `3000`, sometimes more, in order to successfully hack it.
+This will destroy the player's current BitNode.
+
+There is a second method of destroying a BitNode, but it must be unlocked by first destroying BitNode-6 or BitNode-7 ([Bladeburners](bladeburners.md)).
+
+When the player destroys a BitNode, most of their progress will be reset.
+This includes things such as [Augmentations](../basic/augmentations.md) and [RAM](../basic/ram.md) upgrades on the home computer.
+The only things that will persist through destroying BitNodes are:
+
+- [Source-Files](sourcefiles.md)
+- [Scripts](../basic/scripts.md) on the home computer
+- [Intelligence](intelligence.md)

src/Documentation/doc/advanced/bladeburners.md

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+# Bladeburners
+
+PLACEHOLDER

src/Documentation/doc/advanced/gang.md

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+# Gang
+
+Managing a gang can be very rewarding. By rising above all other gangs you get access to almost all augmentations in the game.
+
+PLACEHOLDER

src/Documentation/doc/advanced/grafting.md

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+# Grafting
+
+Grafting is an experimental process through which you can obtain the benefits of [Augmentations](../basic/augmentations.md), without needing to reboot your body.
+
+Grafting can be done at VitaLife in New Tokyo, where you'll find a shady researcher with questionable connections.
+From there, you can spend a sum of money to begin grafting [Augmentations](../basic/augmentations.md).
+This will take some time.
+When done, the [Augmentation](../basic/augmentations.md) will be applied to your character without needing to install.
+
+Be warned, some who have tested grafting have reported an unidentified malware.
+Dubbed `Entropy`, this virus seems to grow in potency as more [Augmentations](../basic/augmentations.md) are grafted, causing unpredictable affects to the victim.
+
+Note that when grafting an [Augmentation](../basic/augmentations.md), cancelling will **not** save your progress, and the money spent will **not** be returned.

src/Documentation/doc/advanced/hacknetservers.md

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+# Hacknet Servers
+
+These are a very powerful upgrade to [Hacknet Nodes](../basic/hacknet_nodes.md).
+Instead of producing money, the Hacknet Servers produce `hashes`.
+This currency can be exchanged for a variety of upgrades that boost most other mechanics of the game.
+
+They can also be used to run scripts on.
+However, this reduces the amount of `hash` produced.

src/Documentation/doc/advanced/intelligence.md

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+# Intelligence
+
+Intelligence is a stat that is unlocked by having [Source-File 5](sourcefiles.md) (i.e. Destroying [BitNode-5](bitnodes.md)).
+
+Intelligence is unique because it is permanent and persistent.
+It never gets reset back to 1.
+However, gaining Intelligence experience is extremely slow.
+It is a stat that gradually builds up as you continue to play the game.
+
+Intelligence will boost your production for many actions in the game, including:
+
+- [Hacking](../basic/hacking.md)
+- [Infiltration](../basic/infiltration.md)
+- [Crime](../basic/crimes.md) success rate
+- [Bladeburner](bladeburners.md) actions
+- [Reputation](../basic/reputation.md) gain for [Companies](../basic//companies.md) & [Factions](../basic/factions.md)
+- [Augmentation](../basic/augmentations.md) [Grafting](grafting.md) speed

src/Documentation/doc/advanced/sleeves.md

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+# Sleeves
+
+When VitaLife unveiled their Persona Core technology that allowed people to digitize and transfer their consciousness into other vessels, human bodies became nothing more than 'sleeves' for the human consciousness.
+This technology thus became known as "Sleeve technology".
+
+Sleeve technology unlocks two different gameplay features:
+
+- Duplicate Sleeves
+- [Grafting](grafting.md)
+
+Sleeve technology is unlocked in [BitNode-10](bitnodes.md).
+
+## Duplicate Sleeves
+
+Duplicate Sleeves are MK-V Synthoids (synthetic androids) into which your consciousness has been copied.
+In other words, these Synthoids contain a perfect duplicate of your mind.
+
+Duplicate Sleeves are essentially clones which you can use to perform work-type actions, such as working for a [Company](../basic/companies.md) / [Faction](../basic/factions.md) or committing a [Crime](../basic/crimes.md).
+When sleeves perform these tasks, they will earn money, experience, and [Reputation](../basic/reputation.md).
+
+Sleeves are their own individuals, which means they each have their own experience and stats.
+
+When a sleeve earns experience, it earns experience for itself, the player's original consciousness, as well as all of the player's other sleeves.
+
+Duplicate Sleeves are **not** reset when installing [Augmentations](../basic/augmentations.md), but they are reset when switching [BitNodes](bitnodes.md).
+
+## Obtaining Duplicate Sleeves
+
+There are two methods of obtaining Duplicate Sleeves:
+
+- Destroy [BitNode-10](bitnodes.md).
+  Each completion gives you one additional Duplicate Sleeve.
+- Purchase Duplicate Sleeves from The Covenant.
+  This is only available in [BitNode-10](bitnodes.md).
+  Sleeves purchased this way are **permanent** (they persist through [BitNodes](bitnodes.md)).
+  You can purchase up to 5 Duplicate Sleeves from The Covenant.
+
+## Synchronization
+
+Synchronization is a measure of how aligned your consciousness is with that of your Duplicate Sleeves.
+It is a numerical value between `1` and `100`, and it affects how much experience is earned when the sleeve is performing a task.
+
+Synchronization can be increased by assigning sleeves to the `Synchronize` task.
+
+## Sleeve Shock
+
+Sleeve shock is a measure of how much trauma the sleeve has due to being placed in a new body.
+It is a numerical value between `0` and `100`, where `100` indicates full shock and `0` indicates no shock.
+Shock affects the amount of experience earned by the sleeve.
+
+Sleeve shock slowly decreases over time.
+You can further increase the rate at which it decreases by assigning sleeves to the `Shock Recovery` task.
+
+Let `X` be the sleeve's shock and `Y` be the sleeve's synchronization.
+When the sleeve earns experience by performing a task, the sleeve gains `X%` of the amount of experience normally earned by the task.
+The player’s original host consciousness and all of the player's other sleeves earn `Y%` of the experience that the sleeve gained, or `X\*Y %` of the normal experience amount.
+
+## Augmentations
+
+You can purchase [Augmentations](../basic/augmentations.md) for your Duplicate Sleeves.
+In order to do this, the sleeve's shock must be at `0`.
+Any [Augmentation](../basic/augmentations.md) that is currently available to you through a faction is also available for your Duplicate Sleeves.
+There are a few [Augmentations](../basic/augmentations.md), such as NeuroFlux Governor and [Bladeburner](bladeburners.md)-specific ones, that cannot be purchased for a Duplicate Sleeve.
+
+When you purchase an [Augmentation](../basic/augmentations.md) for a Duplicate Sleeve, it is instantly installed.
+When this happens, the sleeve's stats are instantly reset back to 0, similar to when you normally install [Augmentations](../basic/augmentations.md).
+
+The cost of purchasing an [Augmentation](../basic/augmentations.md) for a Duplicate Sleeve is **not** affected by how many [Augmentations](../basic/augmentations.md) you have purchased for yourself, and vice versa.
+
+## Memory
+
+Sleeve memory dictates what a sleeve's synchronization will be when it is reset by switching [BitNodes](bitnodes.md).
+For example, if a sleeve has a memory of `10`, then when you switch [BitNodes](bitnodes.md) its synchronization will initially be set to `10`, rather than 1.
+
+Memory can only be increased by purchasing upgrades from The Covenant.
+Just like the ability to purchase additional sleeves, this is only available in [BitNode-10](bitnodes.md).
+
+Memory is a persistent stat, meaning it never gets reset back to `1`.
+The maximum possible value for a sleeve's memory is `100`.
+
+Buying memory has no instant affect on synchronization - memory affects only the starting synchronization upon entering a [BitNode](bitnodes.md).

src/Documentation/doc/advanced/sourcefiles.md

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+# Source-Files
+
+Source-Files are a type of persistent upgrade that is more powerful than [Augmentations](../basic/augmentations.md).
+Source-Files are received by destroying a [Bitnode](bitnodes.md).
+There are many different [BitNodes](bitnodes.md) in the game and each [BitNode](bitnodes.md) will grant a different Source-File when it is destroyed.
+
+A Source-File can be upgraded by destroying its corresponding [BitNode](bitnodes.md) a second or third time (playing through that [BitNode](bitnodes.md) again).
+It can be upgraded to a maximum of level 3, with the exception of Source-File 12, which has no hard limit.

src/Documentation/doc/advanced/stanek.md

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+# Stanek
+
+Allison is a bit crazy.
+But her special [Augmentation](../basic/augmentations.md) is very useful despite its ~~bugs~~ features.
+The Gift consists of a grid of squares in which tetris-like pieces called fragments can be placed.
+Each fragment boost a different player multiplier.
+However, the fragments are not very powerful by themselves.
+
+To increase the power of a fragment, the `ns.stanek.charge()` function needs to be called.
+More threads means more power.
+
+There are also special fragments called booster fragments which increase the power of the fragment it touches.