The only program that fits my workflow for larger (read: multi-chapter) works, and my secondary option for shorter works.

I've used version 0.6.0, for Linux (Mint 18.2) and Windows (7), and just updated to 0.8.0. Most of this was thus written with 0.6.0 in mind, with a few allowances for visible updates.

Pros:

• Markdown. A must for me.
• Ability to export as html, amongst other things.
• Small file size. Default is a program-specific compressed archive file; if you untick the box for that, it's a folder structure where everything is saved as .md files.
• Split-screen option, useful for comparing scenes or checking notes.
• Ability to choose what you can and can't compile (read: export), so you can keep notes mixed in with the final product without affecting it.
• Custom font/background colour options in writing window.
• Cross-platform; consistent between Windows and Linux.
• Option to remember previous project, which can be unticked.
• Option to display/hide wordcount in tree view. If a wordcount goal for a scene/folder is set, also displays a progress bar below the working area.

Cons:

• In 0.6.0, occasionally crashes without warning when trying to, for example, move a folder from one project to another. Not sure if it still does in 0.8.0.
• No program-wide dark theme; UI is consistently light.
• No as-you-write live preview. (I prefer working split-screen edit/preview view where possible.)
• Does not remember the previous save (or load) location for new files; only recent files are remembered. When working on multiple devices, have to open each project on each new device for it to find them again later.
• On Linux, does not support automatically updating.

Other notes:

• Spellcheck doesn't always display red underlines when working in folders (rather than scenes). Clicking into the scene should fix this.
• I have had times when spellcheck has only offered to add words to dictionary when it had suggestions; words it didn't have suggestions for could not be added. (In my case, this included a character name.)
• When working in a folder, does not automatically scroll the view when the cursor goes offscreen.
• Displays markdown marks (eg asterisks) inline, while also showing the formatting. This is my personal preference, but won't be to everyone's taste.
• Font face choices save to the file; if using between multiple devices, all devices must have the font face of choice to display properly, otherwise it reverts to the default (sans serif iirc) font.
• Windows version displays two windows on the taskbar (Win7); one background and one foreground.
• Does not support rich text. Some html support (or at least highlighting).
• Some markdown is displayed with alternate colours, which cannot be changed and may be difficult to read on darker backgrounds.

Manuskript is an amazing software I wish I could use. I love its features and structure. Unfortunately, after a while, I can't open projects anymore. I connected the support but never got an answer.

Great tool for fiction writing minuses: In fullscreen and compile mode text shows without spaces after commas not all compile filters working miss git integration files names stupid on cyrylic

Linux alternative to Scrivener

It looks like a great alternative to Scrivener, but unfortunately you can't use bold or any other code, the software has no ability to hide the code and display only the formatted text, it looks ridiculous.

This is by far the best alternative to Scrivener. It’s only a few features short of outright beating Scrivener. Potential to become the industry standard as soon as it’s stable and with a form of crash rescue or automatic cloud sync.

highly recommended.

This is a pro level creative tool, and it's almost mind-boggling how it's open source and free.