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feat(dotfiles): add merge entries that own only some keys of a config file - #14012
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Included review availability: This review used your included allowance. Your plan provides up to 10 included reviews per hour; 5 remain after this review. 📝 WalkthroughWalkthroughDotfile entries can now merge source-owned keys into JSON, TOML, and YAML targets. The edit system validates and compares structured data, detects conflicting assignments, and leaves merged keys unchanged during unapply. ChangesStructured Dotfile Merge
Priority: ➖ Normal Estimated code review effort: 4 (Complex) | ~45 minutes Change: Feature Sequence Diagram(s)sequenceDiagram
participant EditOp
participant structured_merge
participant TargetFile
EditOp->>structured_merge: parse source and compare shared keys
structured_merge->>EditOp: return comparison or conflict paths
EditOp->>structured_merge: merge source values into target content
structured_merge->>EditOp: return merged content
EditOp->>TargetFile: write merged content
Merge Risk: ⚪ Minimal · up to No actionable merge-blocking issue is established; this change is mergeable after normal checks. 🚥 Pre-merge checks | ✅ 4 | ❌ 1❌ Failed checks (1 warning)
✅ Passed checks (4 passed)
✨ Finishing Touches 💡 1🛠️ Fix failing CI checks 💡
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Review comments at @src/system/edits.rs:
- Around line 749-795: Update same_target to recognize missing targets whose
existing ancestors resolve to the same directory, even when their ancestor path
strings differ; treat identical tails as the same target, while preserving
case-insensitive tail matching only when the ancestor spellings differ only by
case.
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src/system/edits.rs
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… file
Tools like Codex, Claude Code, and oh-my-pi write their own state into the
same JSON, TOML, or YAML file that holds your settings. Symlink and copy
entries fight them for the whole file, and a block can't survive an
application that rewrites the file. A merge entry owns only the keys in its
source:
[dotfiles]
"~/.codex/config.toml/shared" = { source = "codex/shared.toml", merge = true }
Applying sets those keys and leaves everything else, including comments and
key order in TOML and YAML, to the application. `mise dot status` and
`mise dot diff` report drift only in the keys you own, and an unparseable
target is reported instead of overwritten.
Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
Entire-Checkpoint: 01M48J0BNXSK6T94TS7QH7DVJM
…e writing Address review feedback on merge entries: - Two merge entries for one file that set the same key to different values are now refused instead of flipping the value on every apply. - A merge source that does not parse is reported during planning, even when its target does not exist yet, so earlier entries are not left half applied. - A merge source keeps its trailing newline, which can be part of a YAML block scalar. - `mise dot unapply` skips merge entries before looking at their targets. Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com> Entire-Checkpoint: 01M48NAGGKZ920PJ0PHJ0AC1AZ
…y two names Compare merge targets by file identity as well as by path, so a hard link or a case-variant spelling on a case-insensitive filesystem is still recognized as the same file when two entries set one key to different values. Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com> Entire-Checkpoint: 01M48PMK9G8SYJZXYNMF4YZBJT
Compare merge targets with `file::paths_eq` (case-folded on macOS and Windows) as well as by file identity, so a case-variant spelling of a target that does not exist yet is still recognized as the same file. Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com> Entire-Checkpoint: 01M48Q21QA2CHC6XKAS4RJGE4B
…when provable Compare merge targets by file identity when both exist. For a target that does not exist yet, count case variants as the same file only when an existing ancestor spelled two case-only-different ways resolves to one directory, which shows the volume ignores case. Case-sensitive volumes keep `~/App/x.json` and `~/app/x.json` apart instead of reporting a false conflict. Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com> Entire-Checkpoint: 01M48QHZTRFS1NQ55ARBWA6JV6
…g parent Probe whether the volume holding a missing merge target ignores case by checking if a case-swapped spelling of an existing path component still names the same directory. Two missing targets that differ only in the case of their file name now count as one file on a case-insensitive volume, and stay separate on a case-sensitive one, without creating anything. Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com> Entire-Checkpoint: 01M48R4WB6QWVTX08E8GXNY67Y
… file When two merge targets do not exist yet, compare the directories they will be created in by identity, so two spellings of one directory (a symlinked parent, say) with the same file name count as the same target. Case-only differences in the file name still need the volume to be shown to ignore case. Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com> Entire-Checkpoint: 01M48RCWCS1F1PMNBC5B9JKZ2X
Drop the volume case probe from merge target conflict detection. It tested the wrong directory, and a unit test built on it failed on case-insensitive filesystems such as macOS. Existing files are still compared by identity, which covers hard links and case variants of a file that exists; missing files match when they share a name in one directory. A case-only difference in a missing file's name is not guessed at: once the first entry has created the file, a conflicting second entry is compared by identity and refused. Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com> Entire-Checkpoint: 01M48RZ713P13SRF406S6JBWZ7
…skipped `mise dot apply ~/file.toml/a` only sees entry `a`, so a sibling `b` that sets the same key differently went unnoticed and the two flipped the value on alternate applies. Apply now also renders the config's other merge entries for the same file and refuses the pair. Templates of entries that are not being applied are not rendered on a dry run. Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com> Entire-Checkpoint: 01M48TPM31KQ2V3NNYA00DXCTR
Entries a run does not apply were compared with each other, so two disagreeing siblings could block applying a third, unrelated merge. Only the entries being applied are now compared with each other and with the config's other entries for the file. A sibling whose target is blocked, such as a symlink, is skipped before its template is rendered, so its exec() calls do not run. Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com> Entire-Checkpoint: 01M48VBT11WM5N23DZ29DVYQHK
…rge entries A block and a merge that set the same TOML key to different values flipped it on alternate applies, because only merges were compared with each other. A block whose content parses as the merge's format is now compared with the merge too, including against the config's entries a target filter skipped. A merge entry that also carried a whole-file key such as `exclude` was parsed as a whole-file entry as well, so applying it created the target as a directory. A table with `merge` is now only ever an edit, and whole-file keys on it are refused by name. Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com> Entire-Checkpoint: 01M48WJ6HGPVG20GY9HNQ98REV
Comparing a block with a merge treated the block as a standalone document, so it could report a conflict between keys in different tables, and it rendered unselected block templates just to look. Neither is worth blocking an apply over. Merge entries are again compared only with each other, and the docs say not to give a merge and a block the same key. Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com> Entire-Checkpoint: 01M48X565306YXGA47FPQJYQ56
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`mise dot pull` accepted an incoming merge entry that the edit parser would later drop (for example one that also carried `exclude`), so its settings never applied. Incoming merge declarations are now checked the way the edit parser reads them, without rendering templates. Two merge entries that reach one file through different extensions (a hard link under a .json and a .yml name) are refused, since the file cannot be merged consistently as both formats. Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com> Entire-Checkpoint: 01M48Y6S1Y1V2MW1WCNCH6QNMS
The refusal of two merge entries that reach one file as different formats ran only on rendered content, so a dry run skipped it for template entries. The format comes from the target's extension, so it is now checked statically over the requests and the config's other merge entries, including on dry runs. Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com> Entire-Checkpoint: 01M48YP47MFE1VHA0MQRJ65HQ3
An unselected merge entry whose target is a symlink cannot write anything, so it no longer counts toward the different-format refusal. The check skips siblings whose target is blocked, without rendering their templates. Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com> Entire-Checkpoint: 01M48Z5ZDYA7ZRQAE2KBCYBJ6F
The format check ran `precheck`, which reads the target, on every unselected merge entry before asking whether it shares a file with a selected one, so an unrelated target such as a named pipe could hang a filtered apply or a dry run. A sibling's target is now looked at only after it is found to share the file with a different format. Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com> Entire-Checkpoint: 01M48ZQT39B0F12TJSPHX6AVH1
`same_file::is_same_file` opens both paths, so comparing a selected merge target with a sibling that is a named pipe blocked a filtered apply once the selected target existed. Target identity now comes from `stat` (device and inode on Unix), which opens nothing. The e2e test creates the selected target first so it covers this path. Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com> Entire-Checkpoint: 01M4909JA6WZAT3CFZA7N554R7
A filtered apply rendered other merge entries for the same file to look for conflicts, which could run `exec()` in a template nobody asked to apply. Template siblings are now skipped outright; a conflict with one is found when that entry is applied. Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com> Entire-Checkpoint: 01M490STJEB479W0WD34RTKY1W
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Cursor Bugbot has reviewed your changes and found 1 potential issue.
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Reviewed by Cursor Bugbot for commit ff810de. Configure here.
A conflict involving a `template = "tera"` merge entry is found only when every entry in it is applied in the same run, since unselected templates are never rendered. Say so in the code comment and the docs instead of claiming the conflict is found when the template is applied alone. Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com> Entire-Checkpoint: 01M4913YG4SXH6FHCCZCQYQDAF
The schema forbade only some whole-file keys beside `merge = true`, while the
parser refuses all of them, so editors accepted entries such as
`{ source = "s.json", merge = true, enabled = false }` that mise then drops.
List every whole-file key the parser rejects.
Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
Entire-Checkpoint: 01M491MADPW85C9KJWX6DVR5AW
<!-- entire-trail-link-start --> https://entire.io/gh/jdx/mise/trails/430 <!-- entire-trail-link-end --> ### 🚀 Features - **(bootstrap)** add a tool-update service that keeps auto_update tools current by @jdx in [#14040](#14040) - **(config)** add global section write targets by @jdx in [#14018](#14018) - **(config)** move mise's auto-update settings under self_update.* by @jdx in [#14038](#14038) - **(dotfiles)** report notification availability and add notify command by @jdx in [#14009](#14009) - **(dotfiles)** add merge entries that own only some keys of a config file by @jdx in [#14012](#14012) - **(http)** add headers option for bearer and API-key auth by @jdx in [#14022](#14022) - **(install)** add an opt-in identity-based install layout by @jdx in [#13951](#13951) - **(install)** keep identity-layout installations in a shorter directory on Windows by @jdx in [#13952](#13952) - **(installs)** list installations and choose the one requests without a lockfile use by @jdx in [#13953](#13953) - **(installs)** move legacy installations into the identity layout by @jdx in [#13955](#13955) - **(lock)** preserve shared lockfile entries on request by @jdx in [#13980](#13980) - **(npm)** install packages from git repositories by @jdx in [#14044](#14044) - **(prune)** add prune.exclude to keep chosen tools from being pruned by @jdx in [#14030](#14030) - **(secrets)** add [secrets.fnox] project config and mise secrets ls by @jdx in [#13967](#13967) - **(secrets)** add --secrets and --secrets-all to mise run and mise x by @jdx in [#13975](#13975) - **(task)** give tasks only the fnox secrets they list by @jdx in [#13974](#13974) - **(task)** allow {{ secrets.X }} in task env values by @jdx in [#13978](#13978) - **(upgrade)** update global tools before they run with auto_update by @jdx in [#14026](#14026) - **(util)** add a comment-preserving YAML merge helper by @jdx in [#14010](#14010) - **(util)** add format-aware merge for JSON, TOML, and YAML files by @jdx in [#14011](#14011) ### 🐛 Bug Fixes - **(backend)** read a repository's packslip release list once per command by @jdx in [#13991](#13991) - **(backend)** only warn about a backend switch when the backend kind changes by @jdx in [#14032](#14032) - **(bootstrap)** don't create history state or fail on its lock unless writing files by @jdx in [#14029](#14029) - **(cargo)** serialize rustup state across cargo install fallbacks by @jdx in [#14042](#14042) - **(config)** keep global config when a project ignore resolves onto it via symlink by @jdx in [#14006](#14006) - **(doctor)** only warn about backend mismatches the registry serves by @jdx in [#14005](#14005) - **(dotenv)** leave a value ending in escaped whitespace unquoted by @jdx in [#13956](#13956) - **(dotfiles)** explain missing sources in conflicting declaration errors by @himkt in [#13973](#13973) - **(dotfiles)** skip legacy link discovery for group entries by @jdx in [#14023](#14023) - **(dotnet)** disable lockfile url enforcement for dotnet tool backend by @james-newell-forge in [#13971](#13971) - **(env)** fully redact secrets when redaction values overlap by @jdx in [#13962](#13962) - **(github)** log partial attestation verification failures by @jdx in [#14035](#14035) - **(github)** warn when attestations are skipped because the Sigstore trust root is unreachable by @jdx in [#14036](#14036) - **(http)** fetch a cached GitHub release once when callers race by @jdx in [#13990](#13990) - **(http)** don't retry a 429 whose Retry-After outlasts the backoff by @jdx in [#14027](#14027) - **(http)** retry downloads when an HTTP/2 stream reset fails the body read by @jdx in [#14049](#14049) - **(install)** switch backends into a new installation, and resolve CLI-named versions without guessing by @jdx in [#13957](#13957) - **(install)** keep a version incomplete until its postinstall hook succeeds by @jdx in [#14037](#14037) - **(install)** keep incomplete-install markers out of the cache by @jdx in [#14051](#14051) - **(mcp)** reject run_task task names that start with a dash by @jdx in [#13961](#13961) - **(oci)** stream large blob uploads in one PATCH by @jdx in [#14017](#14017) - **(outdated)** don't bump vendor-only requests like java@temurin by @jdx in [#14031](#14031) - **(prune)** keep versions that a running process was started from by @jdx in [#14020](#14020) - **(prune)** snapshot what templated tool versions render to in the identity layout by @jdx in [#14025](#14025) - **(pypi)** build uv tool venvs on mise's python by @jdx in [#14024](#14024) - **(pypi)** lock from <root>/simple/ for JSON URLs by @deiga in [#14007](#14007) - **(python)** create the auto uv venv with mise's python during install by @halms in [#13981](#13981) - **(release)** skip the vfox-tiny test fixture when vendoring embedded plugins by @jdx in [#14047](#14047) - **(ruby)** keep Gemfile reload watches out of executable hooks by @DahanItamar in [#13985](#13985) - **(task)** list monorepo subproject tasks in the mise://tasks MCP resource by @jdx in [#14053](#14053) - **(uninstall)** report each version once in a dry run by @jdx in [#13992](#13992) ### 📚 Documentation - **(http)** show a package proxy recipe for url_replacements by @jdx in [#14050](#14050) - **(readme)** add Star History badges by @jdx in [#13968](#13968) - keep code blocks and alert markers out of llms.txt summaries by @DahanItamar in [#14034](#14034) ### ⚡ Performance - **(secrets)** read cached fnox secrets from the fnox daemon by @jdx in [#13979](#13979) ### 🧪 Testing - **(e2e)** stabilize task timing assertions by @jdx in [#13977](#13977) - **(go)** disable minimum_release_age in go install e2e by @jdx in [#13989](#13989) ### 📦️ Dependency Updates - lock file maintenance by @renovate[bot] in [#13963](#13963) - update github actions by @renovate[bot] in [#13994](#13994) - update rust crates by @renovate[bot] in [#13996](#13996) - update rust crate nodejs-semver to v7 by @renovate[bot] in [#13999](#13999) - update jdx/mise-action action to v5 by @renovate[bot] in [#13997](#13997) - update jdx/renovate-config action to v1.0.2 by @renovate[bot] in [#14003](#14003) - update dependency usage to latest by @renovate[bot] in [#14004](#14004) - update jdx crates to v6.12.1 by @renovate[bot] in [#14002](#14002) - update rust crate sigstore-verify to 0.14 by @jdx in [#14019](#14019) - update rattler by @renovate[bot] in [#13998](#13998) - update rust crate clx to v3.0.4 by @renovate[bot] in [#14028](#14028) ### 📦 Registry - update moved plugin references by @jdx in [#13972](#13972) ### Chore - **(ci)** update pr-closer to v1.3.0 by @jdx in [83f3e90](83f3e90) ### Ci - update pr closer action by @jdx in [#13970](#13970) - add manual M4 sandbox pilot by @jdx in [09e8f8f](09e8f8f) ### Security - **(env)** keep secrets inherited from a parent mise out of templates, caches and other tasks by @jdx in [#13966](#13966) ### New Contributors - @DahanItamar made their first contribution in [#14034](#14034) - @deiga made their first contribution in [#14007](#14007) - @james-newell-forge made their first contribution in [#13971](#13971) ## 📦 Aqua Registry Updates ### New Packages (3) - [`editorconfig/editorconfig-core-go`](https://github.com/editorconfig/editorconfig-core-go) - [`jdx/jactionlint`](https://github.com/jdx/jactionlint) - [`tontinton/maki`](https://github.com/tontinton/maki) ### Updated Packages (3) - [`anchore/syft`](https://github.com/anchore/syft) - [`eksctl-io/eksctl`](https://github.com/eksctl-io/eksctl) - [`regclient/regclient/regsync`](https://github.com/regclient/regclient)

https://entire.io/gh/jdx/mise/trails/461
Tools like Codex, Claude Code, and oh-my-pi write their own state into the same JSON, TOML, or YAML file that holds your settings. A
symlinkorcopydotfile entry fights them for the whole file, and ablockcan't survive an application that rewrites the file. A newmergeedit entry owns only the keys in its source and leaves the rest to the application:With
codex/shared.tomlholdingmodel = "gpt-5"and[tui] theme = "light",mise dot applysets those two keys in~/.codex/config.tomland leaves the app's[plugins.*]tables,notify, and comments exactly where they were. The format comes from the target's extension, and a missing target is created from the source.mise dot statusandmise dot diffreport drift only in owned keys, so keys the application adds never show up.template = "tera"renders the source first, like other edit entries.mise dot unapplyleaves merged keys in place because the application may have changed them.Also teaches the whole-file entry parsers (
files.rs, dotfile groups) thatmergemarks an edit. Without that a merge entry was also read as a whole-file symlink at~/.codex/config.toml/shared, which the new e2e test caught. Addsmergetoschema/mise.jsonand a section todocs/dotfiles.md.Open design questions from the discussion, answered conservatively and easy to change: removing a key from the source does not remove it from the target, and arrays are replaced rather than merged. A modify-script entry (chezmoi's
modify_) is not part of this PR.Verified with the new
e2e/cli/test_dotfiles_merge_edits(create, drift, in-place apply across all three formats, unapply, bad extension, unparseable target), the existing dotfiles edit/files/groups/absent e2e tests, unit tests, andcargo clippy --workspace --all-features --all-targets -- -D warnings.Closes nothing directly; addresses the request in #13986. Stacked on #14011.
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Note
Medium Risk
Changes dotfile apply semantics and writes user config files in place; conflict and parse-failure guards reduce overwrite risk but behavior is new and broadly user-facing.
Overview
Adds
merge = truedotfile edit entries so mise can own only selected keys in JSON, TOML, or YAML targets while apps keep the rest of the file (comments and formatting where supported).The edit engine gains
EditOp::Merge, wired through apply/status/diff/unapply: drift is judged on owned keys viastructured_merge, invalid targets/sources are refused, and unapply leaves merged keys untouched.structured_merge::conflictsdetects when multiple entries set the same dotted path to different values; apply also blocks format mismatches on the same inode/path (hard links, filtered applies) and skips rendering unselected template siblings for conflict checks.Config/schema/docs are updated so
mergeis treated as an edit (not a whole-file entry), with validation on pull and a large e2e suite.Reviewed by Cursor Bugbot for commit a985977. Bugbot is set up for automated code reviews on this repo. Configure here.
Summary by CodeRabbit