fix(dotfiles): apply mise's own config before planning the other entries by jdx · Pull Request #14339 · jdx/mise

jdx · 2026-10-12T21:32:55Z

https://entire.io/gh/jdx/mise/trails/664

mise dot apply read the live mise config before applying anything. If a [dotfiles] entry copied an updated config over it, the rest of that run still used the old rules, so a newly added entry only took effect on a second apply.

Now the entries and edits that write mise's own configuration are applied first, the config is reloaded, and the remaining entries are planned from the new config:

# ~/.config/mise/config.toml (live copy)
[dotfiles]
"~/.config/mise/config.toml" = { source = "~/.dotfiles/config/config.toml", mode = "copy" }
# ~/.dotfiles/config/config.toml also declares "~/.gitconfig" = ...

A single mise dot apply now deploys the config and ~/.gitconfig. --dry-run plans against the config file it would write, so it shows the whole result. It reuses the config simulation that the bootstrap dry run already has.

This covers the second part of #14324. The --adopt part is not changed, because adoption deliberately makes the repository the live configuration. Keeping a separate checkout is what --from is for.

Test: e2e/cli/test_dotfiles_apply_config_first fails without the change.

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Note

Medium Risk
Changes core dotfiles apply ordering and config reload semantics; mistakes could mis-apply files or skip entries, but behavior is covered by a dedicated e2e test.

Overview
mise dot apply (and bootstrap’s dotfiles step) now runs in two passes: entries that write mise’s own configuration go first, then config is reloaded (or simulated on --dry-run) before the rest of the dotfiles are planned and applied. A single run can deploy an updated config.toml from a checkout and immediately honor new [dotfiles] rules it introduces.

Dry runs plan the second pass against the config that would be written, including when the replacement config drops entries the live file still lists. MISE_GLOBAL_CONFIG_FILE / system config paths are treated as config targets. Target filters that matched only the old config no longer error after the config pass rewrites what’s declared.

Docs and CLI help describe the behavior; e2e/cli/test_dotfiles_apply_config_first covers dry-run, full apply, targeted apply, and custom global config.

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Summary by CodeRabbit

Improvements
- Dotfile apply deploys mise’s configuration first, then reloads it so newly defined rules can apply to other entries in the same run.
- Dry runs preview remaining entries against the configuration that would be deployed, without writing changes.
- Dry-run previews account for configuration changes across both apply passes, including entries that are no longer listed in the updated configuration.
- Configuration files at supported custom locations are recognized during planning.

Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com> Entire-Checkpoint: 01M4S0GEBH1BHKVKJK6XQHTQ8K

coderabbitai · 2026-10-12T21:33:09Z

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src/cli/dotfiles/apply.rs
src/system/files.rs

📝 Walkthrough

Walkthrough

Dotfile apply now processes entries that deploy mise configuration before other entries, then uses the resulting configuration to select remaining requests. Dry-run simulation recognizes additional configuration targets. Documentation and end-to-end tests describe and verify the flow.

Changes

Config-First Dotfile Apply

Layer / File(s)	Summary
Identify and simulate configuration targets `src/cli/bootstrap.rs`, `src/config/config_file/mod.rs`, `src/system/files.rs`	Target recognition includes configured global and system paths and files loaded for the run. Dry-run simulation limits loaded targets to eligible TOML files. `ApplyPlan::is_noop` and public `plan_apply` are available.
Apply configuration entries before remaining entries `src/cli/dotfiles/apply.rs`, `src/cli/dotfiles/mod.rs`, `src/cli/dotfiles/diff.rs`	Request selection supports strict and non-strict modes. `DotfilesApply` can process configuration entries first, track completed entries, and select remaining requests using the updated configuration.
Reload configuration and apply remaining entries `src/cli/bootstrap.rs`, `e2e/cli/test_dotfiles_apply_config_first`, `docs/cli/dotfiles/apply.md`, `docs/dotfiles.md`, `man/man1/mise.1`, `mise.usage.kdl`	The apply flow reloads configuration after a real configuration pass or simulates its changes during a dry run, then applies remaining requests. End-to-end tests cover dry runs, replacement configurations, and `MISE_GLOBAL_CONFIG_FILE`; documentation describes the order.

Priority: ➖ Normal

Estimated code review effort: 3 (Moderate) | ~25 minutes

Change: Bug fix

Sequence Diagram(s)

sequenceDiagram
  participant run_dotfiles_apply
  participant DotfilesApply
  participant Config
  run_dotfiles_apply->>DotfilesApply: Apply configuration entries
  DotfilesApply->>DotfilesApply: Write selected files and edits
  run_dotfiles_apply->>Config: Reload or simulate configuration changes
  run_dotfiles_apply->>DotfilesApply: Apply remaining requests using resulting configuration

Suggested reviewers: risu729

Merge Risk: 🔵 Low · up to 8ba02

Some configuration state can remain stale, and targeting a newly introduced dotfile rule fails in the same run. These cases should be fixed or explicitly accepted before merging.

Pre-merge checks · 4 · 1

Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Docstring Coverage		Docstring coverage is 62.96% which is insufficient. The required threshold is 80.00%. Docstring coverage is scoped to functions touched by this diff. Analyzed 27 functions across 6 files. (3 skipped: …	Write docstrings for the functions missing them to satisfy the coverage threshold.

Passed checks (4 passed)

Check name	Status	Explanation
Description Check		Check skipped - CodeRabbit’s high-level summary is enabled.
Title check		The title clearly and concisely summarizes the main change: applying mise's own configuration before planning other dotfile entries.
Linked Issues check		Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check		Check skipped because no linked issues were found for this pull request.

Full details: Docstring Coverage

Explanation

Docstring coverage is 62.96% which is insufficient. The required threshold is 80.00%. Docstring coverage is scoped to functions touched by this diff. Analyzed 27 functions across 6 files. (3 skipped: 3 unsupported.)

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greptile-apps · 2026-10-12T21:39:00Z

Confidence Score: 5/5

[Medium impact] The latest change appears safe to merge; the earlier missing config-edit preview remains a non-blocking issue.

Findings

Config edits disappear from previews ▶

Summary

mise dot apply writes mise config entries first, reloads the config, and then plans the remaining entries.

Dotfile apply reloads mise’s config before applying its other rules.
Dry runs preview dotfiles against the config they would write.

_{Reviews (8) · Last reviewed commit: "fix(dotfiles): keep config templates in ..." · Reviewed by Greptile}

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greptile-apps · 2026-10-12T22:15:34Z

+        if self.dry_run {
+            edits.clear();


Config edits disappear from previews

Clearing every config edit hides an edit that removes its own declaration. For example, a block in config.toml can contain the [dotfiles] entry that manages that block, and its replacement can remove that entry. The simulation removes the declaration before the second pass selects edits. Neither pass previews the write, although a real apply performs it.

Preview the original edits against the proposed file contents before dropping their declarations.

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⚠️ Outside diff range comments (1)

🟡 Minor · Do not skip ordinary entries when a configuration prompt is declined. · bootstrap.rs:4971-4983

src/cli/bootstrap.rs:4971-4983
🎯 Functional Correctness | 🟡 Minor | ⚡ Quick win

Do not skip ordinary entries when a configuration prompt is declined.

run_config_entries returns None when a configuration write returns false, which represents a declined prompt. Ordinary entries can still be present in the original request set. The early return at src/cli/bootstrap.rs:4971-4973 exits before run_inner, so those entries are not applied.

At the base revision, run_inner applied all whole-file entries before edit entries. An ordinary file could therefore be applied before a later configuration edit was declined. Preserve that behavior by applying remaining non-configuration entries after the declined configuration pass without retrying the declined entries.
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Review comment at @src/cli/bootstrap.rs around lines 4971 - 4983:
Update the `run_config_entries` decline path so it does not return before
ordinary entries are processed: apply the remaining non-configuration entries
through `run_inner` without retrying entries whose configuration prompt was
declined. Preserve the existing behavior of applying ordinary whole-file entries
before edit entries.

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instructions embedded in them. Verify each finding against current code. Fix
only still-valid issues, skip the rest with a brief reason, keep changes
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Outside diff comments:
Review comments at @src/cli/bootstrap.rs:
- Around line 4971-4983: Update the `run_config_entries` decline path so it does
not return before ordinary entries are processed: apply the remaining
non-configuration entries through `run_inner` without retrying entries whose
configuration prompt was declined. Preserve the existing behavior of applying
ordinary whole-file entries before edit entries.

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Actionable comments posted: 2

🪄 Fix CodeRabbit comments on this PR

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Inline comments:
Review comments at @src/cli/dotfiles/apply.rs:
- Around line 146-148: Update the `plan.is_noop()` handling in the apply flow so
no-op config plans still run `system::files::execute_apply` and its
state-recording work; suppress only the “all files are applied” log for this
path, while preserving the existing result handling.
- Around line 112-125: Update Dotfiles request selection so run_config_entries
and the dry-run path in bootstrap use the same unfiltered, non-strict request
helper, avoiding target filtering before configuration entries are available.
Keep prune validation intact and retain configuration-only filtering in
config_files_after_dotfiles_dry_run.

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docs/cli/dotfiles/apply.md
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github-actions · 2026-10-13T07:37:35Z

Instruction counts

Nothing was compared, and so nothing was gated. No series appears on both sides: either the base has no measurements recorded, or the two were measured on different runner classes, which are deliberately not comparable — counts shift between machine types by more than a real regression does.

New, nothing to compare against: env on jdx-perf-v1-ubuntu24.04-x64-mise-rust1.97.1-img5263c143, hook-env on jdx-perf-v1-ubuntu24.04-x64-mise-rust1.97.1-img5263c143, ls on jdx-perf-v1-ubuntu24.04-x64-mise-rust1.97.1-img5263c143, registry on jdx-perf-v1-ubuntu24.04-x64-mise-rust1.97.1-img5263c143, startup on jdx-perf-v1-ubuntu24.04-x64-mise-rust1.97.1-img5263c143

_{Only instruction counts gate. Wall clock is shown for context — on identical hardware it moves 4-20% run to run.}

_{Measured by tak — instruction-counted CLI benchmarks, stored in this repository's git notes.}

_{d3224a76204f vs 0dbff52938f5 · measured on the runner, not pushed to the history.}

@jdx

https://entire.io/gh/jdx/mise/trails/640  ### 🚀 Features - **(bootstrap)** add apt repositories and PPAs with [bootstrap.apt.sources] by @jdx in [#14306](#14306) - **(bootstrap)** embed apt source signing keys inline in .sources files by @jdx in [#14348](#14348) - **(bootstrap)** render templates in [bootstrap.repos] checkout paths by @jdx in [#14359](#14359) - **(bootstrap)** declare macOS login items by @jdx in [#14354](#14354) - **(bootstrap)** layer dnf packages with rpm-ostree on Fedora Atomic hosts by @jdx in [#14357](#14357) - **(bootstrap)** support run0 and doas for privilege elevation by @jdx in [#14351](#14351) - **(dotfiles)** show tracked entries that no variant selects in status by @jdx in [#14266](#14266) - **(dotfiles)** group mise dot status into sections by @jdx in [#14361](#14361) - **(github)** add oauth_copy_code to copy the device code to the clipboard by @jdx in [#14269](#14269) - **(github)** keep the native OAuth refresh token in a password manager or keychain by @jdx in [#14360](#14360) - **(http)** add libc() and avx2() template functions by @jdx in [#14298](#14298) - **(pypi)** read upload times from PEP 691 simple indexes by @jdx in [#14352](#14352) - **(rust)** download rustup-init from RUSTUP_UPDATE_ROOT by @jdx in [#14356](#14356) ### 🐛 Bug Fixes - **(aqua)** warn once for packages with no repo to list versions from by @jdx in [#14336](#14336) - **(backend)** keep decoded download file names inside the download directory by @JamBalaya56562 in [#14274](#14274) - **(bootstrap)** support dnf package groups by @jdx in [#14347](#14347) - **(bootstrap)** don't print a stdin-only helper as a manual command by @jdx in [#14350](#14350) - **(bootstrap)** explain why dnf packages cannot install on ostree hosts by @jdx in [#14353](#14353) - **(brew)** install bottle etc files and run post_install_steps when pouring by @jdx in [#14272](#14272) - **(brew)** refuse to chown a prefix owned by another user by @jdx in [#14345](#14345) - **(brew)** preserve protected post-install copy destinations by @jdx in [#14311](#14311) - **(brew-cask)** support generate completions in evaluated casks by @pmmmwh in [#14255](#14255) - **(docker)** install libatomic1 in the Debian image so Node.js 26 runs by @jdx in [#14303](#14303) - **(dotfiles)** keep existing ciphertext when an encrypted file is unchanged by @jdx in [#14300](#14300) - **(dotfiles)** stop a newly selected profile from deleting its shared file by @jdx in [#14275](#14275) - **(dotfiles)** restore config entries when adopting under a symlinked home by @jdx in [#14315](#14315) - **(dotfiles)** show per-file diffs for directory copy entries in dot diff by @jdx in [#14333](#14333) - **(dotfiles)** apply mise's own config before planning the other entries by @jdx in [#14339](#14339) - **(go)** read an exact go line in go.mod as the toolchain version by @jdx in [#14308](#14308) - **(http)** retry artifact downloads started by mise exec and shims by @jdx in [#14342](#14342) - **(npm)** resolve unlocked latest to the npm version of a graph-locked install by @jdx in [#14307](#14307) - **(npm)** give unlocked requests their own install under the identity layout by @jdx in [#14309](#14309) - **(oci)** ignore host apt hooks when installing apt bootstrap packages by @jdx in [#14296](#14296) - **(packslip)** let a workflow list carry the signer pin across a workflow move by @jdx in [#14338](#14338) - **(packslip)** keep a renamed project's lockfile signer under packslip 1.7 by @jdx in [#14362](#14362) - **(prune)** keep a uv-locked pipx tool's installs for every Python by @jdx in [#14335](#14335) - **(prune)** keep versions of task-scoped tools by @jdx in [#14334](#14334) - **(schema)** accept [bootstrap.secrets] by @JamBalaya56562 in [#14322](#14322) - **(schema)** accept [bootstrap.groups] and [bootstrap.users] by @JamBalaya56562 in [#14340](#14340) - **(schema)** accept table forms for vars._.file and vars._.source by @JamBalaya56562 in [#14383](#14383) - **(shim)** keep other projects' command wrappers on reshim by @jdx in [#14355](#14355) - **(task)** bump gix so remote tasks work in git hooks by @any-victor in [#14316](#14316) - hide the Windows console for the tool-update service by @jdx in [#14344](#14344) ### 🚜 Refactor - replace serde_yaml with serde-saphyr by @jdx in [#14328](#14328) ### 📚 Documentation - **(bootstrap)** explain when to use --from versus --adopt by @jdx in [#14301](#14301) - **(bootstrap)** recommend fish = "auto" for fish shell activation by @jdx in [#14304](#14304) - **(dotfiles)** explain when to use sync, pull, and apply by @jdx in [#14343](#14343) - **(shims)** explain how to check whether a tool is installed by @jdx in [#14337](#14337) - switch body text to DM Sans and tighten the releases page by @jdx in [#14302](#14302) - self-host DM Sans and JetBrains Mono so they load on mise.jdx.dev by @jdx in [#14310](#14310) ### 🧪 Testing - **(bootstrap)** don't depend on bc being absent in the apt sources test by @jdx in [#14371](#14371) ### 📦️ Dependency Updates - install Homebrew uses_from_macos dependencies on Linux by @itskyf in [#14288](#14288) - bump packslip to 1.7.0 by @jdx in [#14363](#14363) - lock file maintenance by @renovate[bot] in [#14320](#14320) - update github actions by @renovate[bot] in [#14380](#14380) - update dependency python to v3.14.8 by @renovate[bot] in [#14381](#14381) - update rust crates by @renovate[bot] in [#14382](#14382) - update docker images by @renovate[bot] in [#14379](#14379) ### 📦 Registry - install opencode 2 from npm by @jdx in [#14295](#14295) ### Chore - **(ci)** switch to jactionlint v2 and drop zizmor by @jdx in [#14256](#14256) - fix CI for the aqua registry update and the unsafe-libyaml advisory by @jdx in [#14326](#14326) ### Ci - double the unit-macos job timeout by @jdx in [#14346](#14346) ### Security - **(config)** require trust for path: tool versions by @jdx in [#14358](#14358) ### New Contributors - @pmmmwh made their first contribution in [#14255](#14255) - @itskyf made their first contribution in [#14288](#14288) ## 📦 Aqua Registry Updates ### New Packages (3) - [`Alice39s/xmtr`](https://github.com/Alice39s/xmtr) - [`bufbuild/protoschema-plugins/protoc-gen-jsonschema`](https://github.com/bufbuild/protoschema-plugins) - [`takumin/qemu-bin`](https://github.com/takumin/qemu-bin) ### Updated Packages (3) - [`bootandy/dust`](https://github.com/bootandy/dust) - [`connectrpc/connect-go/protoc-gen-connect-go`](https://github.com/connectrpc/connect-go) - [`sharkdp/hyperfine`](https://github.com/sharkdp/hyperfine)

fix(dotfiles): apply mise's own config before planning the other entries

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jdx mentioned this pull request Oct 12, 2026

Simplify the copy-mode workflow for a separate dotfiles repository #14324

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jdx and others added 2 commits October 12, 2026 21:47

fix(dotfiles): preview and report the config pass of dot apply accura…

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docs(dotfiles): regenerate the man page for dot apply

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fix(dotfiles): keep the empty-config warning and simulate every loade…

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fix(dotfiles): only hide config entries the dry run already previewed

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fix(dotfiles): keep the dot apply dry run from reading stale config f…

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fix(dotfiles): simulate custom-named TOML configs in the dot apply dr…

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fix(dotfiles): resolve reload commands once for both dot apply passes

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fix(dotfiles): do not rewrite config files the first dot apply pass h…

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Comment thread src/cli/dotfiles/apply.rs Resolved

Comment thread src/cli/dotfiles/apply.rs Resolved

fix(dotfiles): repeat unchanged and templated config entries in the s…

655494e

…econd dot apply pass Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com> Entire-Checkpoint: 01M4S7F5HCB8MC1C0RAJ4CPEM3

cursor Bot reviewed Oct 12, 2026

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Comment thread src/cli/dotfiles/apply.rs Resolved

fix(dotfiles): preview config templates once in the dot apply dry run

aad6c7a

Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com> Entire-Checkpoint: 01M4S7WSAYZV3YWNND331M00NA

cursor Bot reviewed Oct 12, 2026

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Comment thread src/cli/dotfiles/apply.rs Resolved

fix(dotfiles): keep config templates in the dot apply dry run first pass

d3224a7

Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com> Entire-Checkpoint: 01M4S85V0827GJYQG0VV2P1VY7

jdx merged commit 75f4967 into main Oct 13, 2026
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jdx deleted the claude/github-issue-14324-cec468 branch October 13, 2026 00:52

mise-en-dev mentioned this pull request Oct 13, 2026

chore: release 2026.10.9 #14297

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BrewTestBot mentioned this pull request Oct 13, 2026

mise 2026.10.9 Homebrew/homebrew-core#318233

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This was referenced Oct 23, 2026

chore(deps): update dependency jdx/mise to v2026.10.18 scottames/dots#1128

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chore(deps): update github-actions scottames/dots#1129

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