feat(bootstrap): add flatpak package support

docs/bootstrap.md

@@ -179,7 +179,7 @@ only want to check one part without installing anything.
 
 | Config                                                         | Use for                                                       |
 | -------------------------------------------------------------- | ------------------------------------------------------------- |
-| [`[bootstrap.packages]`](/bootstrap/packages/)                 | OS packages from apk, apt, dnf, pacman, brew, or mas          |
+| [`[bootstrap.packages]`](/bootstrap/packages/)                 | OS packages from apk, apt, dnf, pacman, brew, flatpak, or mas |
 | [`[bootstrap.repos]`](/bootstrap/repos.html)                   | Git repos cloned before dotfiles are applied                  |
 | [`[dotfiles]`](/dotfiles.html)                                 | Whole-file dotfiles and small managed edits to existing files |
 | [`[bootstrap.mise_shell_activate]`](/bootstrap/shell.html)     | mise activation snippets in shell startup files               |

docs/bootstrap/packages/flatpak.md

@@ -0,0 +1,42 @@
+# Flatpak
+
+Flatpak applications and runtimes installed system-wide via the
+[`flatpak`](https://docs.flatpak.org/en/latest/flatpak-command-reference.html) CLI.
+
+```toml
+[bootstrap.packages]
+"flatpak:org.mozilla.firefox" = "latest"
+"flatpak:org.gnome.Builder" = "latest"
+```
+
+Flatpak packages are part of `[bootstrap.packages]`, just like apt packages,
+Homebrew formulae, and Mac App Store apps. The package name is an application
+or runtime ID accepted by `flatpak install` and `flatpak update`.
+
+mise does not install Flatpak or configure remotes implicitly. Install the
+`flatpak` CLI and add the required remote (commonly Flathub) before applying
+the config:
+
+```sh
+flatpak remote-add --if-not-exists flathub https://flathub.org/repo/flathub.flatpakrepo
+mise bootstrap packages use flatpak:org.mozilla.firefox
+```
+
+## Commands
+
+```sh
+mise bootstrap packages status --manager flatpak
+mise bootstrap packages apply --manager flatpak
+mise bootstrap packages upgrade --manager flatpak
+```
+
+mise manages the system-wide Flatpak installation. `apply` runs
+`flatpak install --system --noninteractive <id>` for missing packages, while
+`upgrade` runs `flatpak update --system --noninteractive <id>` for installed
+packages. Flatpak resolves the configured ID from the system remotes.
+
+Flatpak does not expose installation of arbitrary historical versions through
+these commands, so version pins are not supported. Use `"latest"` in config.
+
+The manager is Linux-only and requires `flatpak` on `PATH`. On other platforms,
+or when the command is missing, shared configs list Flatpak entries as skipped.

docs/bootstrap/packages/index.md

@@ -13,6 +13,7 @@ mise can ensure machine-global system packages are installed via the
 "brew:postgresql@17" = "latest"
 "brew:ffmpeg" = "latest"
 "brew-cask:firefox" = "latest"
+"flatpak:org.mozilla.firefox" = "latest"
 "mas:497799835" = "latest"
 ```
 
@@ -42,15 +43,16 @@ declarative sections work the same way:
 
 ## Supported package managers
 
-| Manager     | Platform                                                       | Page                                      |
-| ----------- | -------------------------------------------------------------- | ----------------------------------------- |
-| `apk`       | Alpine Linux                                                   | [apk](/bootstrap/packages/apk.html)       |
-| `apt`       | Debian, Ubuntu                                                 | [apt](/bootstrap/packages/apt.html)       |
-| `dnf`       | Fedora, RHEL, CentOS, Rocky, Alma                              | [dnf](/bootstrap/packages/dnf.html)       |
-| `pacman`    | Arch, Manjaro                                                  | [pacman](/bootstrap/packages/pacman.html) |
-| `brew`      | macOS (arm64), Linux (x86_64/arm64) — **no Homebrew required** | [brew](/bootstrap/packages/brew.html)     |
-| `brew-cask` | macOS — **no Homebrew required**                               | [brew](/bootstrap/packages/brew.html)     |
-| `mas`       | macOS with the `mas` CLI on `PATH`                             | [mas](/bootstrap/packages/mas.html)       |
+| Manager     | Platform                                                       | Page                                        |
+| ----------- | -------------------------------------------------------------- | ------------------------------------------- |
+| `apk`       | Alpine Linux                                                   | [apk](/bootstrap/packages/apk.html)         |
+| `apt`       | Debian, Ubuntu                                                 | [apt](/bootstrap/packages/apt.html)         |
+| `dnf`       | Fedora, RHEL, CentOS, Rocky, Alma                              | [dnf](/bootstrap/packages/dnf.html)         |
+| `pacman`    | Arch, Manjaro                                                  | [pacman](/bootstrap/packages/pacman.html)   |
+| `brew`      | macOS (arm64), Linux (x86_64/arm64) — **no Homebrew required** | [brew](/bootstrap/packages/brew.html)       |
+| `brew-cask` | macOS — **no Homebrew required**                               | [brew](/bootstrap/packages/brew.html)       |
+| `flatpak`   | Linux with the `flatpak` CLI on `PATH`                         | [Flatpak](/bootstrap/packages/flatpak.html) |
+| `mas`       | macOS with the `mas` CLI on `PATH`                             | [mas](/bootstrap/packages/mas.html)         |
 
 ## Semantics
 
@@ -64,7 +66,8 @@ declarative sections work the same way:
 - **OS-filtered** — entries for a manager that isn't available on the current
   machine are not acted on, so the same config works across platforms: `apt`
   entries are ignored on macOS, `dnf` entries on Ubuntu, and so on. `brew`
-  works on both macOS and Linux; `brew-cask` works on macOS; `mas` works on
+  works on both macOS and Linux; `brew-cask` works on macOS; `flatpak` works
+  on Linux when the `flatpak` CLI is on `PATH`; `mas` works on
   macOS when the `mas` CLI is on `PATH`. Status commands still list
   unavailable managers so nothing is silently invisible.
 - **Manual installation only** — mise never installs system packages
@@ -96,7 +99,7 @@ mise bootstrap packages apply --yes     # skip the confirmation prompt
 mise bootstrap packages apply --manager apt
 mise bootstrap packages apply --update  # refresh package manager metadata first
 
-mise bootstrap packages use apk:zlib-dev apt:curl brew:jq brew-cask:firefox mas:497799835
+mise bootstrap packages use apk:zlib-dev apt:curl brew:jq brew-cask:firefox flatpak:org.mozilla.firefox mas:497799835
 mise bootstrap packages use -g brew:ffmpeg     # write globally
 mise bootstrap packages use apt:curl@8.5.0-2   # pin a version
     # (brew pins via the formula name instead: brew:postgresql@17)
@@ -112,6 +115,7 @@ mise bootstrap packages prune --manager brew --yes
 mise bootstrap packages upgrade           # upgrade installed packages to current versions
 mise bootstrap packages upgrade --manager brew
 mise bootstrap packages upgrade --manager brew-cask
+mise bootstrap packages upgrade --manager flatpak
 mise bootstrap packages upgrade --manager mas
 ```
 
@@ -139,12 +143,12 @@ declarative cleanup command, similar in spirit to
 `mise bootstrap packages upgrade` refreshes package manager metadata and upgrades the
 configured packages that are already installed to the newest available
 version — apk, apt, and dnf also honor a version pinned in config (pacman, brew,
-brew-cask, and mas [can't install pins](/bootstrap/packages/pacman.html), so
+brew-cask, flatpak, and mas [can't install pins](/bootstrap/packages/pacman.html), so
 pinned entries are skipped with a warning). Packages that aren't installed
 yet are skipped — that's `mise bootstrap packages apply`'s job. For brew
 this pours the formula's current bottle and replaces the old keg; for
-brew-cask this installs the current cask artifact; for mas this runs
-`mas upgrade`.
+brew-cask this installs the current cask artifact; for flatpak this updates the
+configured applications and runtimes; for mas this runs `mas upgrade`.
 
 `mise doctor` also reports configured system packages and warns when any are
 missing.

docs/cli/bootstrap/packages/apply.md

@@ -26,7 +26,7 @@ Packages in `manager:package` form; defaults to everything configured in [bootst
 
 ### `-m --manager <MANAGER>`
 
-Only install packages for this manager, e.g. `apk`, `apt`, `brew`, `brew-cask`, or `mas`
+Only install packages for this manager, e.g. `apk`, `apt`, `brew`, `brew-cask`, `flatpak`, or `mas`
 
 **Choices:**
 
@@ -35,6 +35,7 @@ Only install packages for this manager, e.g. `apk`, `apt`, `brew`, `brew-cask`,
 - `brew`
 - `brew-cask`
 - `dnf`
+- `flatpak`
 - `mas`
 - `pacman`
 
@@ -54,7 +55,7 @@ Examples:
 
 ```
 mise bootstrap packages apply
-mise bootstrap packages apply apk:zlib-dev apt:curl brew:jq brew-cask:firefox mas:497799835
+mise bootstrap packages apply apk:zlib-dev apt:curl brew:jq brew-cask:firefox flatpak:org.mozilla.firefox mas:497799835
 mise bootstrap packages apply --dry-run
 mise bootstrap packages apply --manager apt --yes
 ```

docs/cli/bootstrap/packages/upgrade.md

@@ -11,7 +11,7 @@ Refreshes package manager metadata and upgrades the configured packages
 that are already installed: apk/apt/dnf/pacman upgrade to the newest available
 version (apk, apt, and dnf honor a version pinned in config), brew pours the
 formula's current bottle and replaces the old keg, brew-cask installs
-the current cask artifact, and mas upgrades App Store apps. Packages that
+the current cask artifact, flatpak updates applications and runtimes, and mas upgrades App Store apps. Packages that
 are not installed yet are skipped — use `mise bootstrap packages apply`
 for those.
 
@@ -27,7 +27,7 @@ Packages in `manager:package` form; defaults to everything configured in [bootst
 
 ### `-m --manager <MANAGER>`
 
-Only upgrade packages for this manager, e.g. `apk`, `apt`, `brew`, `brew-cask`, or `mas`
+Only upgrade packages for this manager, e.g. `apk`, `apt`, `brew`, `brew-cask`, `flatpak`, or `mas`
 
 **Choices:**
 
@@ -36,6 +36,7 @@ Only upgrade packages for this manager, e.g. `apk`, `apt`, `brew`, `brew-cask`,
 - `brew`
 - `brew-cask`
 - `dnf`
+- `flatpak`
 - `mas`
 - `pacman`
 

docs/cli/bootstrap/packages/use.md

@@ -48,7 +48,7 @@ Skip the confirmation prompt
 Examples:
 
 ```
-mise bootstrap packages use apk:zlib-dev apt:curl brew:jq brew-cask:firefox mas:497799835
+mise bootstrap packages use apk:zlib-dev apt:curl brew:jq brew-cask:firefox flatpak:org.mozilla.firefox mas:497799835
 mise bootstrap packages use -g brew:postgresql@17
 mise bootstrap packages use apt:curl@8.5.0-2
 ```

docs/tool-plugin-development.md

@@ -378,7 +378,7 @@ Optional fields:
 
 - **`version`** — a constraint (`>=3.0`, `>3`, `<=1.2`, `=3.0`, or a bare `3.0` meaning `>=3.0`) for `bin` and `pkgconfig`. mise runs `<bin> --version` / `pkg-config --modversion` and compares. If a version can't be extracted, the dependency is treated as satisfied (presence is enough) rather than blocking the install.
 - **`optional`** — a short reason string. Missing optional dependencies never prompt or fail; they surface as a single informational line, letting users build without features they don't need (e.g. Erlang's `wxWidgets` GUI).
-- **`packages`** — a map of package-manager name (`brew`, `brew-cask`, `apt`, `dnf`, `pacman`, `apk`, `mas`) to the package that provides the capability.
+- **`packages`** — a map of package-manager name (`brew`, `brew-cask`, `apt`, `dnf`, `pacman`, `apk`, `flatpak`, `mas`) to the package that provides the capability.
 
 **Detection is the source of truth.** A check that passes is satisfied no matter how the capability was installed — Homebrew, apt, nix, MacPorts, or from source all pass without ceremony, and mise never asks _how_ it got there. The `packages` map is only consulted to _offer_ installing the missing subset; it is a remediation hint, not a declaration that the tool must come from that package manager.
 

man/man1/mise.1

@@ -1056,7 +1056,7 @@ only. `install` is accepted as an alias for this command.
 .PP
 .TP
 \fB\-m, \-\-manager\fR \fI<MANAGER>\fR
-Only install packages for this manager, e.g. `apk`, `apt`, `brew`, `brew\-cask`, or `mas`
+Only install packages for this manager, e.g. `apk`, `apt`, `brew`, `brew\-cask`, `flatpak`, or `mas`
 .TP
 \fB\-n, \-\-dry\-run\fR
 Print the commands that would run without running them
@@ -1191,7 +1191,7 @@ Refreshes package manager metadata and upgrades the configured packages
 that are already installed: apk/apt/dnf/pacman upgrade to the newest available
 version (apk, apt, and dnf honor a version pinned in config), brew pours the
 formula's current bottle and replaces the old keg, brew\-cask installs
-the current cask artifact, and mas upgrades App Store apps. Packages that
+the current cask artifact, flatpak updates applications and runtimes, and mas upgrades App Store apps. Packages that
 are not installed yet are skipped — use `mise bootstrap packages apply`
 for those.
 
@@ -1203,7 +1203,7 @@ Packages can also be given explicitly in `manager:package` form.
 .PP
 .TP
 \fB\-m, \-\-manager\fR \fI<MANAGER>\fR
-Only upgrade packages for this manager, e.g. `apk`, `apt`, `brew`, `brew\-cask`, or `mas`
+Only upgrade packages for this manager, e.g. `apk`, `apt`, `brew`, `brew\-cask`, `flatpak`, or `mas`
 .TP
 \fB\-n, \-\-dry\-run\fR
 Print the commands that would run without running them

mise.usage.kdl

@@ -493,14 +493,14 @@ only. `install` is accepted as an alias for this command.
 Examples:
 
     $ mise bootstrap packages apply
-    $ mise bootstrap packages apply apk:zlib-dev apt:curl brew:jq brew-cask:firefox mas:497799835
+    $ mise bootstrap packages apply apk:zlib-dev apt:curl brew:jq brew-cask:firefox flatpak:org.mozilla.firefox mas:497799835
     $ mise bootstrap packages apply --dry-run
     $ mise bootstrap packages apply --manager apt --yes
 
 """#
-            flag "-m --manager" help="Only install packages for this manager, e.g. `apk`, `apt`, `brew`, `brew-cask`, or `mas`" {
+            flag "-m --manager" help="Only install packages for this manager, e.g. `apk`, `apt`, `brew`, `brew-cask`, `flatpak`, or `mas`" {
                 arg <MANAGER> {
-                    choices apk apt brew brew-cask dnf mas pacman
+                    choices apk apt brew brew-cask dnf flatpak mas pacman
                 }
             }
             flag "-n --dry-run" help="Print the commands that would run without running them"
@@ -625,7 +625,7 @@ Refreshes package manager metadata and upgrades the configured packages
 that are already installed: apk/apt/dnf/pacman upgrade to the newest available
 version (apk, apt, and dnf honor a version pinned in config), brew pours the
 formula's current bottle and replaces the old keg, brew-cask installs
-the current cask artifact, and mas upgrades App Store apps. Packages that
+the current cask artifact, flatpak updates applications and runtimes, and mas upgrades App Store apps. Packages that
 are not installed yet are skipped — use `mise bootstrap packages apply`
 for those.
 
@@ -642,9 +642,9 @@ Examples:
     $ mise bootstrap packages upgrade --dry-run
 
 """#
-            flag "-m --manager" help="Only upgrade packages for this manager, e.g. `apk`, `apt`, `brew`, `brew-cask`, or `mas`" {
+            flag "-m --manager" help="Only upgrade packages for this manager, e.g. `apk`, `apt`, `brew`, `brew-cask`, `flatpak`, or `mas`" {
                 arg <MANAGER> {
-                    choices apk apt brew brew-cask dnf mas pacman
+                    choices apk apt brew brew-cask dnf flatpak mas pacman
                 }
             }
             flag "-n --dry-run" help="Print the commands that would run without running them"
@@ -669,7 +669,7 @@ a mise version selector. mas uses numeric ADAM IDs and does not support pins.
             after_long_help #"""
 Examples:
 
-    $ mise bootstrap packages use apk:zlib-dev apt:curl brew:jq brew-cask:firefox mas:497799835
+    $ mise bootstrap packages use apk:zlib-dev apt:curl brew:jq brew-cask:firefox flatpak:org.mozilla.firefox mas:497799835
     $ mise bootstrap packages use -g brew:postgresql@17
     $ mise bootstrap packages use apt:curl@8.5.0-2
 

src/cli/system/install.rs

@@ -30,8 +30,8 @@ pub struct SystemInstall {
     #[clap(value_name = "PACKAGE")]
     packages: Vec<String>,
 
-    /// Only install packages for this manager, e.g. `apk`, `apt`, `brew`, `brew-cask`, or `mas`
-    #[clap(long, short, value_parser = ["apk", "apt", "brew", "brew-cask", "dnf", "mas", "pacman"])]
+    /// Only install packages for this manager, e.g. `apk`, `apt`, `brew`, `brew-cask`, `flatpak`, or `mas`
+    #[clap(long, short, value_parser = ["apk", "apt", "brew", "brew-cask", "dnf", "flatpak", "mas", "pacman"])]
     manager: Option<String>,
 
     /// Print the commands that would run without running them
@@ -384,7 +384,7 @@ static AFTER_LONG_HELP: &str = color_print::cstr!(
     r#"<bold><underline>Examples:</underline></bold>
 
     $ <bold>mise bootstrap packages apply</bold>
-    $ <bold>mise bootstrap packages apply apk:zlib-dev apt:curl brew:jq brew-cask:firefox mas:497799835</bold>
+    $ <bold>mise bootstrap packages apply apk:zlib-dev apt:curl brew:jq brew-cask:firefox flatpak:org.mozilla.firefox mas:497799835</bold>
     $ <bold>mise bootstrap packages apply --dry-run</bold>
     $ <bold>mise bootstrap packages apply --manager apt --yes</bold>
 "#

src/cli/system/upgrade.rs

@@ -10,7 +10,7 @@ use crate::system;
 /// that are already installed: apk/apt/dnf/pacman upgrade to the newest available
 /// version (apk, apt, and dnf honor a version pinned in config), brew pours the
 /// formula's current bottle and replaces the old keg, brew-cask installs
-/// the current cask artifact, and mas upgrades App Store apps. Packages that
+/// the current cask artifact, flatpak updates applications and runtimes, and mas upgrades App Store apps. Packages that
 /// are not installed yet are skipped — use `mise bootstrap packages apply`
 /// for those.
 ///
@@ -23,8 +23,8 @@ pub struct SystemUpgrade {
     #[clap(value_name = "PACKAGE")]
     packages: Vec<String>,
 
-    /// Only upgrade packages for this manager, e.g. `apk`, `apt`, `brew`, `brew-cask`, or `mas`
-    #[clap(long, short, value_parser = ["apk", "apt", "brew", "brew-cask", "dnf", "mas", "pacman"])]
+    /// Only upgrade packages for this manager, e.g. `apk`, `apt`, `brew`, `brew-cask`, `flatpak`, or `mas`
+    #[clap(long, short, value_parser = ["apk", "apt", "brew", "brew-cask", "dnf", "flatpak", "mas", "pacman"])]
     manager: Option<String>,
 
     /// Print the commands that would run without running them

src/cli/system/use.rs

@@ -140,7 +140,7 @@ impl SystemUse {
 static AFTER_LONG_HELP: &str = color_print::cstr!(
     r#"<bold><underline>Examples:</underline></bold>
 
-    $ <bold>mise bootstrap packages use apk:zlib-dev apt:curl brew:jq brew-cask:firefox mas:497799835</bold>
+    $ <bold>mise bootstrap packages use apk:zlib-dev apt:curl brew:jq brew-cask:firefox flatpak:org.mozilla.firefox mas:497799835</bold>
     $ <bold>mise bootstrap packages use -g brew:postgresql@17</bold>
     $ <bold>mise bootstrap packages use apt:curl@8.5.0-2</bold>
 "#