[jdx]

https://entire.io/gh/jdx/mise/trails/465

mise prune treats a version as unused when no tracked config or tool stub resolves to it. A program started before its version was replaced can still be running from that version — a terminal session still on claude@2.1.289 after claude@2.1.291 is selected, for example — and pruning deletes files out from under the live process. This also applies to the deferred pruning after mise upgrade once upgrade.prune_after has passed. Some setups turn automatic pruning off entirely because of this, and old versions pile up instead.

Pruning now keeps a version while a process is running from it, and says which process kept it. This works on Linux, macOS and Windows:

$ mise prune --tools --dry-run
mise claude@2.1.289 is kept: still running as pid 3445962 (claude)
mise claude@2.1.263 is prunable: claude is required at 2.1.291 by ~/.config/mise/config.toml
mise claude@2.1.263 [dryrun]             uninstall
...

Once the process exits, the version becomes prunable again.

What counts as running from a version

A process runs from an install directory when either of these is inside it:

• its executable, which covers native tools such as claude, gh or node
• an absolute path in its command line, which covers interpreted tools whose executable is an interpreter from another install, such as an npm: or pipx: tool

Install paths are matched both as mise names them and with symlinks resolved. On Windows, matching ignores case.

A command-line path can also go through one of the tool's runtime links. mise puts installs/<tool>/latest/bin on PATH for a latest request, so an npm: tool started that way has installs/npm-foo/latest/... in its command line, and an upgrade later retargets latest while the process keeps running from the old version. If the link has not changed since the process started, it is followed to the version it names. If it changed after the process started, the version the process started from cannot be known, so every prune candidate of that tool is kept until the process exits.

Processes are read from /proc on Linux, libproc and sysctl (KERN_PROCARGS2) on macOS, and the Toolhelp and NtQueryInformationProcess APIs on Windows. Processes that cannot be inspected, such as another user's, are skipped, and a debug line reports how many there were. On Windows this also avoids a prune that fails partway through because the OS refuses to delete a running executable.

Where it applies

The check is part of toolset::prunable_tools, so every command that decides what is unused agrees: mise prune, mise unuse --prune, mise ls --prunable, and the deferred pruning after mise upgrade, which keeps the receipt and checks again at most once a day. mise uninstall and mise upgrade --prune are unchanged; they remove what they are told to remove.

The scan runs only when there are prune candidates.

Tests

• Unit tests in src/toolset/running.rs start real child processes: detection by executable, by command line, no match on a sibling version whose name is a prefix (1.0.1 vs 1.0.10), a symlinked install path, following an unchanged runtime link, and keeping the old version when latest is retargeted after the process started. They run on Linux and macOS; Windows has its own set (executable, quoted command-line paths in any case, sibling prefix, command-line splitting).
• e2e/cli/test_prune_running_process covers mise prune, --dry-run, --dry-run-code and ls --prunable while a process runs from dummy@1.0.0, then pruning after it exits, plus an upgrade with upgrade.prune_after = "0s" keeping the receipt until the process exits. Verified locally on macOS.
• cargo clippy --workspace --all-features --all-targets -- -D warnings is clean on macOS. The Windows module was type-checked for x86_64-pc-windows-msvc but not run locally; the Windows unit tests run in CI.

Based on #14015 by @atoslins, who found the problem and wrote the Linux implementation.

AI-assisted — Tool: Claude Code; model: anthropic/claude-sonnet-5-5; version: unavailable.

🤖 Generated with Claude Code

---

Note

Medium Risk
Pruning now enumerates OS processes and can retain versions longer; incorrect detection could leave stale installs, but the change reduces risk of deleting files under live processes.

Overview
Pruning and post-upgrade deferred removal no longer delete a tool version while a live process still runs from that install directory (executable or absolute script path in the command line, including runtime links like latest).

A new cross-platform running-process scan (toolset/running — /proc on Linux, libproc/sysctl on macOS, Toolhelp/NtQueryInformationProcess on Windows) feeds prunable_tools_with_sources, which now returns a PrunableTools struct with versions held by running PIDs. mise prune logs up to three keeping processes per version; tool purgatory keeps receipts until those processes exit.

Docs (prune, man, usage KDL, upgrade.auto_prune settings) and an e2e test (test_prune_running_process) document and verify the behavior. mise uninstall and mise upgrade --prune are unchanged.

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Summary by CodeRabbit

• New Features

  • Pruning now retains tool versions used by running processes, preventing their files from being removed while they’re in use.
  • Prune results identify retained versions and show up to three processes using each version, with a count of any additional processes.
  • Deferred pruning accounts for running processes and can remove a version after its last process exits.

• Documentation

  • Updated mise prune and automatic pruning guidance to explain how running processes affect version retention.

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📝 Walkthrough

Walkthrough

Process detection now identifies installed tool versions used by running processes on Linux, macOS, and Windows. Pruning excludes those versions and reports why they remain installed. End-to-end tests cover direct pruning and deferred pruning after an upgrade.

Changes

Running-process version retention

Layer / File(s)	Summary
Process detection Cargo.toml, src/toolset/mod.rs, src/toolset/running*.rs	Adds platform-specific process listings and matches executable paths, command-line paths, and runtime links to installed tool versions.
Prune retention and reporting src/toolset/mod.rs, src/cli/prune.rs, src/tool_purgatory.rs	Prune results now include versions retained because processes are running. The CLI reports retained versions and up to three associated processes per version.
Prune validation and documentation e2e/cli/test_prune_running_process, docs/cli/prune.md, man/man1/mise.1, mise.usage.kdl, settings.toml	End-to-end tests cover direct and deferred pruning. CLI and setting documentation describe process-based retention.

Priority: ➖ Normal

Estimated code review effort: 4 (Complex) | ~45 minutes

Change: Bug fix

Sequence Diagram(s)

sequenceDiagram
  participant PruneCLI
  participant Toolset
  participant ProcessDetection
  participant OSProcessListing
  PruneCLI->>Toolset: Request prune results
  Toolset->>ProcessDetection: Check deletion candidates
  ProcessDetection->>OSProcessListing: List processes and start times
  OSProcessListing-->>ProcessDetection: Process paths and start times
  ProcessDetection-->>Toolset: Return versions matched to processes
  Toolset-->>PruneCLI: Return deletion and retention results
  PruneCLI->>PruneCLI: Report retained versions and processes

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Merge Risk: ⚪ Minimal · up to e6aed

The change keeps tool versions installed while a running process uses them, and it reports which process is using each one. No merge-blocking risk was found in the reviewed portions. Only part of the change was supplied for review.

🚥 Pre-merge checks | ✅ 4 | ❌ 1

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Docstring Coverage	⚠️ Warning	Docstring coverage is 43.75% which is insufficient. The required threshold is 80.00%. Docstring coverage is scoped to functions touched by this diff. Analyzed 64 functions across 7 files.	Write docstrings for the functions missing them to satisfy the coverage threshold.

✅ Passed checks (4 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title clearly summarizes the main change: preventing pruning of versions used by running processes.
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.

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Actionable comments posted: 1

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Inline comments:
Review comments at @src/toolset/running_windows.rs:
- Around line 143-173: Update absolute_paths to parse Windows command-line
arguments using CommandLineToArgvW rules, including backslash escaping before
quotes, rather than toggling quote state on every quote. If using the Windows
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add coverage for an escaped quote and a trailing backslash-quote case.

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• settings.toml
• src/cli/prune.rs
• src/tool_purgatory.rs
• src/toolset/mod.rs
• src/toolset/running.rs
• src/toolset/running_linux.rs
• src/toolset/running_macos.rs
• src/toolset/running_windows.rs

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[greptile-apps]

Confidence Score: 5/5

[Medium risk] Adds process tracking to prevent pruning of in-use tool versions.

The PR appears safe to merge, with no outstanding findings.

What we checked:

• Windows decoding stays unchanged: as_chunks::<2>().0 keeps the same complete byte pairs as the previous conversion. The repository already uses this API and requires Rust 1.95.

Summary

Pruning keeps tool versions used by running processes and reports which processes kept them. Deferred pruning keeps checking those versions after the grace period.

• Since the last review, only the Windows byte-pair conversion changed. It preserves the previous behavior.
• The earlier FreeBSD test issue is fixed: the process tests now run only on Linux and macOS.
• No new actionable issues or repository-rule violations were found.

_{Reviews (3) · Last reviewed commit: "fix(prune): satisfy clippy chunks_exact_..."}

[github-actions]

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.}

_{97ba8e9725ae vs 97e0cf6521c2 · measured on the runner, not pushed to the history.}