# Oxygen user guide

This guide is organised by task. It assumes the `oxy` binary is on your

path (`cargo build --release` puts it in `target/release/`). The design

behind every command is in [spec.md](spec.md); this guide only tells you

what to type and what to expect.

Oxygen tracks *changes* rather than snapshots: a change is the set of

edits you made, it commutes with unrelated changes, and conflicts are

recorded in history instead of blocking you. Two ideas recur below:

- A **bookmark** (default `main`) names a *state*: the set of changes it

  contains. A state can have several **heads** when independent changes

  have not been related to each other; that is normal, not a problem.

- The **working copy** is itself a change that Oxygen rewrites every time

  it looks at your files. `oxy commit` turns it into a real change.

Output uses colour and glyphs on a terminal; pipe it, pass `--plain`, or set

`NO_COLOR` for plain ASCII.

## 1. Set yourself up

```

oxy identity create --name "Ada Lovelace" --email [email protected]

oxy config --user core.sign change

```

`identity create` generates a composite Ed25519 + ML-DSA-65 key pair, keeps

the secret in `~/.config/oxy/keys/`, and records you as the default author

in `~/.config/oxy/config.toml`. With `core.sign = change` every commit is

signed; without it, changes are sealed in batches when you push (also

authenticated, just later). Use `--local` to record the identity in one

repository only.

`oxy identity show` prints the key, its expiry, delegates, and whether the

secret is available. `oxy identity export` writes the public identity to a

file to hand to whoever manages a trust policy (section 8).

## 2. Start a repository

```

mkdir project && cd project

oxy init

oxy status

```

`oxy init` creates `.oxy/`. Add `.oxyignore` (gitignore syntax, per

directory, negations with `!`) for files that should never be tracked;

`/target` and `*.tmp` are typical entries. As in Git, ignore rules only

affect untracked files: a file already in history stays tracked until you

delete it.

To take over an existing Git project, see section 12.

## 3. Everyday work

```

oxy status                 # what changed since the last commit

oxy diff                   # the edits, file by file

oxy commit -m "Add retry loop"

oxy log                    # newest first; -n 10, -v for full messages

oxy show 658990aa          # one change by ChangeId prefix, #hash prefix, or @

```

Commit part of what changed with `oxy commit PATH.. -m "..."` (only those

paths; the rest stays as uncommitted work) or `oxy commit -i -m "..."`, which

offers each hunk in turn like `git add -p`; a hunk that another chosen hunk

needs, such as the directory a new file lives in, comes along by itself.

`status --json` prints the same for tools, with every conflict's kind, path and

contributing ChangeIds. On a terminal, `status` lists each path with a mark: `✚ added`, `✎ modified`, `✖ removed`,

`➜ renamed`, `⚙ mode`. Renames are detected: a removed file and an added

file of the same kind whose contents are at least half alike are recorded

as a move of the same file, so identity survives a rename.

Files containing NUL bytes are stored whole ("opaque"); text files are

stored line by line and merge line by line. `.oxyattributes` overrides the

guess (section 14).

Every change has two names: a **ChangeId** (`658990aa…`) that survives

rewrites, and a content hash (`#7469d16c…`) that changes when the change is

edited. Use whichever you have; prefixes work.

## 3a. Bookmarks: branches without merges

A bookmark names a state; each workspace works on one (`main` to begin

with). Because changes commute, "merging" is the union of two bookmarks'

heads, with no merge change and any real conflict recorded as in section 6.

```

oxy bookmark create feature        # at the working copy's base

oxy bookmark switch feature        # check it out; commits now go here

oxy commit -m "Feature work"

oxy bookmark switch main

oxy merge feature                  # main now holds both; working copy follows if clean

oxy bookmark list                  # ● current, heads, ↑n/↓n against origin

oxy push -b feature                # publish a bookmark other than the current one

oxy bookmark set feature 658990aa  # move it; oxy bookmark delete feature to drop it

```

`oxy checkout feature` materialises a bookmark without switching to it, and

a bookmark name works wherever a change is expected when it has one head.

Each workspace remembers its own bookmark, so two directories can sit on

two bookmarks of one repository.

### A develop / feature flow

Names with `/` work everywhere, pushing included:

```

oxy bookmark create feature/42-login          # at the working copy's base

oxy bookmark switch feature/42-login --carry  # started already? take the edits along

oxy commit -F msg.txt                         # a long message from a file

oxy push -b feature/42-login

oxy bookmark switch develop

oxy merge feature/42-login                    # the working copy follows when it was clean

oxy push                                      # develop, with the feature in it

oxy bookmark delete feature/42-login          # oxy push --delete feature/42-login on the remote

```

`bookmark switch` stops when the working copy has uncommitted edits, so

nothing is lost by accident. There are two ways past it:

- `--carry` takes the edits along. It is refused only when the target

  bookmark has other versions of the files they touch.

- `--discard` drops the edits.

`oxy describe` names what the working copy holds, for build stamps:

- a tag, when a tag holds exactly this state;

- otherwise the nearest tag with the distance from it and the change;

- or, with no tag behind it, the bookmark and the change;

- with `-dirty` added when there are uncommitted edits.

## 4. Fix up history

Oxygen keeps its own record of every operation, so all of these are safe to

try and to undo.

```

oxy describe -m "Better message"        # reword the head the working copy sits on

oxy describe 658990aa -m "..."          # reword any change; dependents are rewritten

oxy amend                               # fold the working copy into the head

oxy amend --into 658990aa               # fold it into an older change

oxy split 658990aa src/parser.rs        # split a head: those paths become a separate first change

oxy abandon 658990aa                    # drop a change; its content stays on disk

oxy squash 658990aa --into 9df9ac29     # fold a change into one it depends on

oxy rebase 658990aa --onto feature      # re-express a change against another base

oxy undo                                # undo the last operation, whatever it was

oxy op log                              # the operation log

```

Rewriting a change that others depend on rewrites them too, keeping their

ChangeIds. Because unrelated changes already coexist, `rebase` is rarely

needed; its job is to change what a change is said to build on, for instance

to drop a dependency on something you are about to abandon. Where a dependent referred to a line that no longer exists, the

reference is re-anchored to the nearest surviving line and `oxy abandon`

prints a note about it.

## 4a. Who wrote this, and what broke it

```

oxy blame src/parser.rs          # every line: the change that introduced it, author, age

oxy blame src/parser.rs --json

```

Blame is exact: each line is an atom that remembers the change that

introduced it, so renames cost nothing and there is no heuristic.

```

oxy bisect start

oxy bisect good v1.2             # a change, bookmark or tag known to be fine

oxy bisect bad main              # and one known to be broken

oxy bisect run make test         # exit 0 good, 125 skip, anything else bad

oxy bisect reset                 # back to where you were

```

Without `run`, each step checks out a state to test and you answer with

`oxy bisect good`, `bad`, or `skip`. The candidates are the changes the bad

state has that the good one lacks, ordered so every tested state is

well-formed; the answer is the first change whose inclusion breaks things.

## 5. Move around

```

oxy checkout                    # the bookmark's heads

oxy checkout 658990aa           # the state of one change and its dependencies

oxy checkout v1.2               # a tag

oxy checkout --discard ...      # throw away uncommitted work first

```

Checking out a single older change gives you the files that change and its

dependencies touch, not a full snapshot from that date: in Oxygen a change

depends only on what it actually builds on.

## 6. Conflicts

A conflict never stops a commit, fetch, or pull. It is recorded in the

state and shown by `oxy status`, which exits with status 2 while any

conflict remains. Conflicted text files are written with markers:

```

<<<<<<< oxy conflict 1 of 2, side 1: change k7m2p9 "Add retry loop"

... lines ...

======= oxy conflict 1 of 2, side 2: change q3x8w1 "Refactor client"

... lines ...

>>>>>>> oxy conflict 1 of 2 end

```

Edit the file to what it should be (keep one side, both, or neither) and

remove the markers. Tree conflicts, such as two files wanting the same

name, appear as `<name>.oxy-conflict-<n>` candidates: keep the one you

want under the right name and delete the rest.

```

oxy resolve      # which conflicts your edits resolve, which still have markers

oxy commit -m "Resolve retry vs refactor"

```

The commit is recorded as a *resolution*, a change that depends on every

side of the conflict; anyone who fetches it gets the conflict resolved.

## 7. Work with others

Run a server (any machine with the repositories under one directory):

```

oxy serve --root /srv/oxy --bind 0.0.0.0:8890 --token SECRET \

          --tls-cert cert.pem --tls-key key.pem

```

Without `--tls-*` the server speaks plain HTTP; keep that on a loopback

address or behind a TLS terminator. `--token` makes pushes require a bearer

token; reads stay open.

On your machine:

```

oxy clone https://host:8890/project

cd project

oxy config remote.origin.token SECRET   # or export OXY_TOKEN

oxy config remote.origin.ca my-ca.pem   # self-signed server: extra roots to trust (or OXY_CA)

oxy push

oxy pull

```

- `oxy fetch` updates `origin/main` without touching your bookmark.

- `oxy pull` fetches, then makes your bookmark the union of both sides.

  There is no merge commit; unrelated changes simply coexist, and a real

  conflict is recorded as in section 6. The working copy follows when it was

  clean.

- `oxy push` sends your changes and moves the remote bookmark. If the remote

  moved since you last fetched, the push is refused: pull and push again.

  `--force` overrides the compare-and-swap.

- `oxy remote add|remove|list` manages remotes; the clone source is `origin`.

A repository can also be cloned from a local path, which is handy for tests

and for a bare "hub" on a shared disk.

## 8. Decide who may publish: the trust policy

Without a policy a repository is *unverified*: everything is accepted and

every remote command says so. A policy names root keys and the keys allowed

to update each bookmark; servers and clients enforce it.

```

oxy policy init                    # your key becomes the only root; push publishes it

oxy policy show

oxy policy grant alice.identity    # alice.identity came from her `oxy identity export`

oxy policy grant ci.identity --pattern 'release/*'

oxy policy revoke 9458b656         # by KeyId prefix

oxy verify                         # signature status of every change in the log

```

Several people can hold root keys:

```

oxy policy root add bob.identity

oxy policy root threshold 2        # future updates need two root signatures

```

Once the threshold is above one, an update you make alone becomes a

*proposal file* (`policy-<serial>.proposal`, or `--out`). Send it to another

root holder, who runs `oxy policy sign policy-7.proposal`; whoever completes

the threshold applies it, and the next push publishes it. Everyone else

picks it up on fetch, verifying each step from the policy they already

trust.

## 9. Keys over time

```

oxy identity rotate                   # fresh key pair; old signatures stay valid

oxy identity renew --expires 365      # same keys, new expiry in days (0 = never)

oxy identity delegate add ci.identity # let another key sign on your behalf

oxy identity delegate remove 3f2a…

oxy identity revoke                   # retire your own key

oxy identity revoke 3f2a… --reason "laptop stolen"   # any key, if you hold a root

```

Rotation, renewal, and delegation all issue a successor identity that names

the previous one. If a policy names your key, it is updated to the successor

in the same step (as a proposal when more root signatures are needed).

Changes signed before the rotation remain authorised; a revoked key

authorises nothing. `oxy verify` shows signatures by revoked keys as valid

but revoked.

## 10. Tags and workspaces

```

oxy tag create v1.2 -m "First release"   # the current heads; or name changes

oxy tag list

oxy workspace add ../project-hotfix      # a second checkout sharing the repository

oxy workspace list

oxy workspace forget ../project-hotfix

```

A tag is an immutable state, signed when you have a key, and travels with

push and fetch. Workspaces have their own working copy and bookmark

(`workspace.bookmark`) but share objects and history.

### Receipts from CI

A runner such as OxygenFlow signs a receipt for every job it runs: what ran,

in what environment, on which files, and the result. Receipts are kept with

the state they ran on.

```

oxy receipt list                         # receipts for the bookmark's state

oxy receipt show 3f2a9c                  # one in full, with its signature checked

oxy receipt export 3f2a9c build.receipt  # hand it to someone

oxy receipt verify build.receipt         # check one without keeping it

oxy receipt import build.receipt         # verify and keep it

```

## 11. Big repositories: partial, sparse, shallow

```

oxy clone URL --max-blob 1M          # files above 1 MiB are fetched on first read

oxy clone URL --sparse src --sparse docs   # materialise only these subtrees

oxy clone URL --depth 50             # only the last 50 levels of history

oxy sparse src docs tests            # change the filter later

oxy deepen 100                       # fetch more history below the boundary

```

Lazy blobs and sparse trees do not affect commits: what you do not have is

left exactly as it was. A shallow clone starts from a *checkpoint* of the

state, so status and commit work at full speed from the first minute.

## 11a. Nested repositories (submodules)

A subrepo is another repository checked out at a path and pinned to a state,

Oxygen or Git. The pin is versioned like a file, so two people pinning

different states get an ordinary conflict.

```

oxy submodule add https://host/lib.git libs/lib     # Git or Oxygen URL; records .oxymodules

oxy commit -m "Add lib"                              # the pin is committed with the parent

oxy submodule status                                 # pin vs what is on disk

oxy submodule update --init                          # after a clone: fetch nested repositories

oxy submodule remove libs/lib                        # drop the node; the directory stays

```

Committing the parent records whatever the nested repository is at, and

checking out an older parent state moves the nested repository back, unless

it has uncommitted changes, which are never overwritten. An absent nested

repository keeps its pin until you run `update --init`. Git submodules

survive `oxy git import` as Git pins and go back out as gitlinks on export.

## 12. Git interoperability

```

oxy git import ../project.git ./project-oxy --branch main   # convert a Git history

oxy git fetch https://github.com/you/project.git            # bring new Git commits in

oxy git push  https://github.com/you/project.git            # publish your changes to Git

oxy git export ../mirror.git                                # a plain Git mirror of the bookmark

```

Import turns each commit into one change (merge commits become

resolutions), keeps authors and hashes as `Git-Author`/`Git-Commit`

trailers, detects renames, and skips submodules. `git fetch`/`git push` keep

a bare mirror under `.oxy/git/`; a push is refused until the remote's tip

has been fetched, so it always fast-forwards. Exported commits carry

`Change-Id` and `Oxy-Hash` trailers.

## 13. Automate: hooks

Executables in `.oxy/hooks/<event>` (never cloned) receive one JSON object

on stdin. `pre-commit`, `pre-push` and other `pre-*` hooks veto by exiting

non-zero, and their stderr becomes the error message. Events:

`pre-commit`, `post-commit`, `pre-push`, `post-fetch`, `post-checkout`, and

`semantic-deps`, which runs at commit when `hooks.semantic-deps = true` and

answers `{"deps": ["<hash>", …]}` to make the change depend on more than it

textually references.

## 14. Per-path attributes, ignores, locks

`.oxyattributes` uses gitattributes syntax:

```

*.png     binary

*.txt     text eol=lf

*.psd     lockable nocompress

```

`binary`/`text` override content sniffing, `eol=lf|crlf` normalises line

endings in the store and on checkout, `nocompress` stores chunks raw, and

`lockable` files are checked out read-only until you take the local lock:

```

oxy lock assets/logo.psd

oxy unlock assets/logo.psd

```

Locks are advisory and local; server-side locks are planned.

## 15. Configuration

Two files, both `key = "value"` lines: `~/.config/oxy/config.toml`

(`oxy config --user KEY VALUE`) and `.oxy/config` (`oxy config KEY VALUE`).

The repository file wins. `OXY_HOME` relocates the user directory. `OXY_TIMINGS=1` prints how long each phase of a snapshot takes (loading the base state, rendering it, reading the working copy, building the change) to standard error, for finding out where a slow command spends its time.

| Key | Meaning |

|---|---|

| `author.name`, `author.email`, `author.key` | who you are; `key` is set by `identity create` |

| `core.sign` | `change` to sign every commit; otherwise seals at push |

| `core.op-retention` | days for which old operations keep their states alive (90) |

| `core.gc-grace` | days an unreachable object survives (14) |

| `core.checkpoint-interval` | changes between automatic checkpoints (256) |

| `filter.max-blob`, `filter.paths` | lazy blobs and sparse subtrees (section 11) |

| `hooks.semantic-deps` | run the semantic-deps hook at commit |

| `workspace.bookmark` | this workspace's bookmark (`main`) |

| `remote.<name>.url`, `.token`, `.ca` | remotes; token and CA fall back to `OXY_TOKEN` and `OXY_CA` |

## 16. Shell prompt

`oxy prompt` prints `main 658990aa*+2` (bookmark, working copy, `*` dirty,

`!` conflicted, ahead/behind origin) in a few milliseconds and records

nothing. See [prompt.md](prompt.md) for bash, oh-my-bash, zsh, and fish

snippets and the `--format` placeholders.

## 17. Housekeeping

```

oxy gc              # pack loose objects, prune unreachable ones past the grace period

oxy gc --now        # ignore the grace period (only when nothing else is writing)

oxy fsck            # check every object, the op log, references, signatures, checkpoints

oxy doctor          # check identity, config and remotes, with what to do about each problem

oxy checkpoint      # serialise the bookmark's state so large histories load instantly

```

Both run automatically: packing when loose objects pile up, checkpoints

every `core.checkpoint-interval` changes.

## 17a. Scripting and editors

Every reporting command takes `--json` (`status`, `log --path`, `show`,

`diff`, `hunks`, `blame`, `resolve`, `op log`, `bookmark list`, `remote list`,

`fetch`, `pull`, `push`, `submodule status`, `bisect status`, `verify`,

`policy show`, `root`, `version`). `oxy cat PATH -r CHANGE` prints a file as

it was, `oxy discard PATH..` restores files to the base, and `oxy hunks`

numbers the working copy's hunks for `commit --hunks` and `discard --hunks`.

## 18. If something looks wrong

- **"the remote has change … which you do not; pull first"**: someone

  pushed since your last fetch. `oxy pull`, then push.

- **"policy needs N root signature(s)"** on fetch: the server's policy was

  updated in a way your copy cannot verify. Ask a root holder whether the

  chain of updates was published; a fresh clone trusts the current policy.

- **`oxy status` exits 2**: conflicts remain; see section 6.

- **Many heads on `main`**: independent changes that do not reference one

  another. Nothing to fix; the state is their union.

- **Undo anything**: `oxy undo` reverts the last operation, including

  pulls, checkouts, and rewrites.

## Shell completions and man pages

```sh

oxy completions bash > ~/.local/share/bash-completion/completions/oxy   # bash

oxy completions zsh > "${fpath[1]}/_oxy"                                 # zsh

oxy completions fish > ~/.config/fish/completions/oxy.fish               # fish

oxy man --dir ~/.local/share/man/man1                                    # then: man oxy-commit

```

The oh-my-bash plugin in `contrib/oh-my-bash` loads the bash completions itself.