feat: set-up — /etc/environment + /etc/profile root patches (PR-6c) (#38)

* feat: set-up subcommand — MVP scaffold + lifecycle hooks (PR-6a)

Implements the core value of `set-up` per
`docs/subcommand-specs/set-up/SPEC.md`: convert an already-running container
into a DevContainer by applying configuration + image metadata and executing
lifecycle hooks, emitting a single-line JSON result on stdout.

## CLI surface

`deacon set-up --container-id <id> [--config <path>] [--skip-post-create]
[--skip-non-blocking-commands] [--remote-env NAME=VALUE]...
[--include-configuration] [--include-merged-configuration]
[--container-data-folder <path>]`

## What this PR includes

- `--container-id` resolution + inspect validation. Missing container fails
  with the upstream-aligned summary `"Dev container not found."`
- Optional `--config` load via `ConfigLoader::load_with_extends` (extends
  chain honored per CLAUDE.md). Missing path fails with
  `"Dev container config (<path>) not found."`
- Image-metadata extraction from the container's `devcontainer.metadata`
  label. Tolerates BOTH the JSON-array form (PR-2 / #27) and the
  single-object form for older images.
- Config merge: file config wins over image metadata on scalar fields
  (spec §4 `mergeConfiguration(config.config, imageMetadata)`).
- Variable substitution for both `configuration` and `mergedConfiguration`.
- Lifecycle hook execution via `ContainerLifecycle` (onCreate →
  updateContent → postCreate → postStart → postAttach), gated by
  `--skip-post-create` (skips ALL phases per spec §2) and
  `--skip-non-blocking-commands` (stops after the configured `waitFor`).
- JSON output per spec §10: `{outcome: "success", configuration?,
  mergedConfiguration?}`. `containerId` is intentionally excluded (spec
  §16 design decision).

## Deferred to PR-6b

- `/etc/environment` + `/etc/profile` root-side patches with system markers
  under `/var/devcontainer/`
- Dotfiles installer with target-path marker (would reuse
  `crates/deacon/src/commands/up/dotfiles.rs`)
- A second substitution pass against the live container environment
  (`${containerEnv:VAR}`) — current pass uses the configured
  `container_env`, not a live `docker exec` env probe

These are spec §5 phases 3a and 3c; both marked "best-effort" with graceful
fallback on failure. Splitting them out keeps PR-6a reviewable.

## Tests

14 new unit tests in `set_up::tests`:
- `--remote-env` parsing (accepts `NAME=VALUE`, rejects malformed input)
- `--config` loading (default when absent, error when missing path)
- Image-metadata label parsing (missing → None, array form, single-object
  form, invalid JSON → error)
- Config merging (file wins over metadata; file-only when no metadata)
- Argument defaults and JSON-result shape (outcome field, optional fields)

Verification:
- `cargo fmt --all -- --check`
- `cargo clippy --all-targets -- -D warnings`
- `cargo test -p deacon --lib` → 227 pass
- `make test-nextest-fast` → 1927 pass (no regression)

Refs: issue #34 (Tier 1 progress tracker), plan
`/home/vscode/.claude/plans/let-s-come-up-with-recursive-sutherland.md`
(PR-6 sequencing rationale).

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* feat: set-up — wire dotfiles installer (PR-6b)

Follow-up to PR-6a (#36). Adds the three `--dotfiles-*` flags from spec §2
to the `set-up` CLI surface and threads them as a `DotfilesConfig` into
`ContainerLifecycle`. The lifecycle helper already implements clone +
auto-detected installer (`install.sh` / `bootstrap` / `setup` / `script/*`)
+ target-path marker for idempotency — set-up just needed to opt in.

## New flags

- `--dotfiles-repository <URL or owner/repo>`
- `--dotfiles-install-command <string>` (overrides auto-detection)
- `--dotfiles-target-path <path>` (defaults to `~/dotfiles`)

No repository → no clone. The lifecycle helper's marker-at-target-path
guard provides idempotency across re-runs (spec §6, §16 design decision).

## Tests

3 new unit tests in `set_up::tests::build_dotfiles_config_*`:

- `returns_none_when_no_repository` — no repo URL means no opt-in, even if
  the other flags are set
- `forwards_all_three_fields` — all flags round-trip into `DotfilesConfig`
- `leaves_defaults_to_lifecycle_helper` — `target_path` / `install_command`
  stay `None` so the helper computes its standard defaults

Verification:
- `cargo fmt --all -- --check`
- `cargo clippy --all-targets -- -D warnings`
- `cargo test -p deacon --lib set_up` → 17 pass (14 from PR-6a + 3 new)

## Deferred to PR-6c

- `/etc/environment` + `/etc/profile` root-side patches with system markers
  under `/var/devcontainer/` (spec §5 phase 3a; net-new code that needs
  root exec + heredoc plumbing)
- Live-container `${containerEnv:VAR}` second-pass substitution

Refs: issue #34 (Tier 1 progress tracker); PR-6a (#36).

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* feat: set-up — /etc/environment + /etc/profile root patches (PR-6c)

Follow-up to PR-6b (#37). Implements spec §5 phase 3a: append-only root
patches to `/etc/environment` and `/etc/profile` so login shells inherit
the resolved container env / PATH. Both patches are guarded by marker
files under `--container-system-data-folder` (default `/var/devcontainer/`)
so re-running set-up against the same container is a no-op.

## What this PR adds

- **New CLI flag**: `--container-system-data-folder <path>` (spec §6,
  default `/var/devcontainer`).
- **`apply_etc_patches`** wires both patches before the lifecycle hook
  phase (spec §5 puts system patches in phase 3a). Skipped when
  `--skip-post-create` is set, mirroring upstream's "post-create is the
  umbrella for user customization" semantics.
- **`build_etc_environment_patch_script`**: emits a shell script that
  appends a `# >>> deacon set-up >>>` ... `# <<< deacon set-up <<<`
  block of `KEY="VALUE"` lines to `/etc/environment`. Escapes `\` and
  `"` so the PAM parser doesn't choke. Touches the marker only after a
  successful append. Empty env → no-op (does NOT touch the marker, so a
  later run with a populated config still patches).
- **`build_etc_profile_patch_script`**: emits a shell script that
  re-exports PATH from `/etc/environment` inside a delimited block. This
  is the spec-§16 design-decision recipe — without it the env appended
  in `/etc/environment` doesn't reach login shells.
- **`collect_env_pairs`**: merges `containerEnv` + `remoteEnv` + CLI
  `--remote-env` overlays into a sorted, deterministic list. CLI wins on
  key conflicts. `None`-valued `remote_env` entries are dropped.
- **Best-effort**: any non-zero exit from the patch shell (no root,
  read-only `/etc`, missing `sh`, etc.) emits a WARN and proceeds. Spec §9:
  system-level patches "do not abort set-up unless critical".

## Tests

10 new unit tests:
- `build_etc_environment_patch_returns_noop_when_env_empty`
- `build_etc_environment_patch_short_circuits_when_marker_present`
- `build_etc_environment_patch_writes_sorted_env_block`
- `build_etc_environment_patch_wraps_block_in_delimiters`
- `build_etc_environment_patch_escapes_special_chars_in_values`
- `build_etc_profile_patch_short_circuits_on_marker`
- `build_etc_profile_patch_reexports_path_from_environment`
- `build_etc_profile_patch_wraps_in_delimiters`
- `collect_env_pairs_merges_config_remote_and_cli`
- `collect_env_pairs_returns_sorted_output`

Total set-up tests: 27 pass (14 from PR-6a + 3 from PR-6b + 10 new).

Verification:
- `cargo fmt --all -- --check`
- `cargo clippy --all-targets -- -D warnings`
- `cargo test -p deacon --lib` → 240 pass (no regression)

## With this PR, the set-up subcommand is functionally complete

The only spec-§5 item still on the deferred list is the live-container
`${containerEnv:VAR}` second-pass substitution — an enhancement, not a
behavior gap; the configured `container_env` is already substituted.

Refs: issue #34 (Tier 1 progress tracker); PR-6a (#36), PR-6b (#37).

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

---------

Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

Author: pofallon

crates/deacon/src/cli.rs

@@ -582,6 +582,10 @@ pub enum Commands {
         /// Inside-container user data root (default `~/.devcontainer`).
         #[arg(long)]
         container_data_folder: Option<PathBuf>,
+        /// Inside-container system data root for root-owned marker files
+        /// (default `/var/devcontainer`). Spec §6.
+        #[arg(long)]
+        container_system_data_folder: Option<PathBuf>,
     },
 
     /// Run user-defined lifecycle commands
@@ -1512,6 +1516,7 @@ impl Cli {
                 include_configuration,
                 include_merged_configuration,
                 container_data_folder,
+                container_system_data_folder,
             }) => {
                 use crate::commands::set_up::{execute_set_up, SetUpArgs};
 
@@ -1530,6 +1535,7 @@ impl Cli {
                     include_merged_configuration,
                     container_data_folder: container_data_folder
                         .or_else(|| self.container_data_folder.clone()),
+                    container_system_data_folder,
                     docker_path: self.docker_path.clone(),
                     progress_tracker: progress_tracker.clone(),
                 };