Clean up Decodex CLI argument ownership

README.md

@@ -85,9 +85,9 @@ without publishing every low-level or skipped item to the static site or Git his
 - The Decodex runtime contract is Unix-only: macOS and Linux.
 - Windows is outside the runtime contract.
 - The public site is static and deploys through GitHub Pages.
-- Starting `decodex serve` without `--config` loads enabled projects from the explicit
-  registry only. It does not scan Codex history, repo-local config files, or currently
-  open worktrees to infer projects.
+- Starting `decodex serve` without its `--config` option loads enabled projects from
+  the explicit registry only. It does not scan Codex history, repo-local config files,
+  or currently open worktrees to infer projects.
 
 ## Usage
 
@@ -106,6 +106,9 @@ cargo run -p decodex --bin decodex -- run --dry-run
 cargo run -p decodex --bin decodex -- serve --interval 60s --listen-address 127.0.0.1:8912
 ```
 
+Project-scoped commands accept `--config <PROJECT_DIR>` after the subcommand when the
+operator wants to override registry-based project resolution for that command.
+
 ### Install from Source
 
 ```sh
@@ -147,8 +150,8 @@ matching `accounts.jsonl` entry.
 `~/.codex/decodex/agent-evidence/<service-id>/` and prints the same handoff index for
 repair agents.
 
-`decodex maintenance prune --dry-run` reports local Decodex storage retention
-candidates without applying retention changes. Add `--apply` to rotate
+`decodex maintenance prune` defaults to the same read-only report as
+`decodex maintenance prune --dry-run`. Add `--apply` to rotate
 oversized local logs and agent-evidence event streams, prune old backup files, compact
 old terminal-run protocol events after preserving their summary, and checkpoint the
 SQLite WAL. `decodex serve` also runs the auto-safe subset at startup and periodically

apps/decodex-app/README.md

@@ -13,10 +13,10 @@ The first Decodex App release manages the shared Codex account pool through the
 bundled Rust app helper so account UI stays on the same CLI-owned files even when a
 long-running local `decodex serve` is older than the app bundle. On launch the app also
 connects to an existing `decodex serve` on the default local endpoint when one is
-available; otherwise it starts the bundled `decodex serve --api-only` binary for
-operator snapshot and WebUI routes. App-started servers do not poll registered projects
-or dispatch Linear work. The helper owns account operations and interactive login flows
-that need streamed command output:
+available; otherwise it starts the bundled Decodex binary in its hidden API-only
+operator endpoint mode for operator snapshot and WebUI routes. App-started servers do
+not poll registered projects or dispatch Linear work. The helper owns account
+operations and interactive login flows that need streamed command output:
 
 - list accounts without printing token material
 - pin future Decodex runs to one account

apps/decodex/src/archive_hygiene.rs

@@ -47,7 +47,7 @@ pub(crate) fn run(config_path: Option<&Path>, request: &ArchiveHygieneRequest) -
 	let state_store = runtime::open_runtime_store()?;
 	let Some(config_path) = resolve_config_path(config_path, &state_store)? else {
 		eyre::bail!(
-			"No Decodex project config found. Pass --config <PROJECT_DIR> or register one with `decodex project add <PROJECT_DIR>`."
+			"No Decodex project config found. Pass this command's --config <PROJECT_DIR> or register one with `decodex project add <PROJECT_DIR>`."
 		);
 	};
 	let config = ServiceConfig::from_path(&config_path)?;