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Apply shfmt formatting and configure MegaLinter shfmt style - #3869

#3869
Open
plengauer with Copilot wants to merge 2 commits into
mainplengauer/Thoth:mainfrom
copilot/fix-shfmt-formatting-issuesplengauer/Thoth:copilot/fix-shfmt-formatting-issuesCopy head branch name to clipboard
Open

Apply shfmt formatting and configure MegaLinter shfmt style#3869
plengauer with Copilot wants to merge 2 commits into
mainplengauer/Thoth:mainfrom
copilot/fix-shfmt-formatting-issuesplengauer/Thoth:copilot/fix-shfmt-formatting-issuesCopy head branch name to clipboard

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Copilot AI commented Jul 27, 2026

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MegaLinter's shfmt reported formatting diffs on ~60% of shell files because no shfmt configuration existed — shfmt's tab-indent defaults conflicted with the codebase's 2-space style.

Changes

  • .mega-linter.yml (new): sets SHELL_SHFMT_ARGUMENTS: "-i 2 -ci" (2-space indent, indented case bodies) to match house style; also adds SPELL_LYCHEE_FILTER_REGEX_EXCLUDE to skip lychee URL checks on .github/workflows/
  • .gitattributes: marks demos/injection_deep_gradle/gradlew as linguist-generated to exclude the Gradle wrapper boilerplate from linting
  • actions/instrument/job/decorate_action.sh: fixes shebang from #!/bin/sh#!/bin/bash — the file already used bash-only features (${!1}, $'\n') that prevented shfmt from parsing it in POSIX mode
  • 74 shell files: reformatted with shfmt -w -i 2 -ci — purely cosmetic (redirect operator spacing, case pattern alignment, ;; placement)

@plengauer

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Hello, thanks for contributing for the first time!

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MegaLinter analysis: Error

Descriptor Linter Files Fixed Errors Warnings Elapsed time
❌ COPYPASTE jscpd yes 70 no 1.36s
✅ REPOSITORY betterleaks yes no no 5.85s
❌ REPOSITORY checkov yes 1 1 24.11s
❌ REPOSITORY devskim yes 2027 185 133.48s
✅ REPOSITORY dustilock yes no no 0.94s
✅ REPOSITORY gitleaks yes no no 71.21s
✅ REPOSITORY git_diff yes no no 0.11s
❌ REPOSITORY grype yes 2 no 115.54s
❌ REPOSITORY kingfisher yes 1 4 22.19s
❌ REPOSITORY osv-scanner yes 4 no 3.79s
✅ REPOSITORY secretlint yes no no 4.8s
✅ REPOSITORY syft yes no no 8.71s
❌ REPOSITORY trivy yes 11 6 11.45s
✅ REPOSITORY trivy-sbom yes no no 0.89s
✅ REPOSITORY trufflehog yes no no 5.13s

Detailed Issues

❌ REPOSITORY / checkov - 1 error
usage: checkov [-h] [-v] [--support] [-d DIRECTORY] [--add-check]
               [-f FILE [FILE ...]] [--skip-path SKIP_PATH]
               [--external-checks-dir EXTERNAL_CHECKS_DIR]
               [--external-checks-git EXTERNAL_CHECKS_GIT]
               [--external-checks-public-key EXTERNAL_CHECKS_PUBLIC_KEY] [-l]
               [-o {cli,csv,cyclonedx,cyclonedx_json,json,junitxml,github_failed_only,gitlab_sast,sarif,spdx}]
               [--output-file-path OUTPUT_FILE_PATH] [--output-bc-ids]
               [--include-all-checkov-policies] [--quiet] [--compact]
               [--framework FRAMEWORK [FRAMEWORK ...]]
               [--skip-framework SKIP_FRAMEWORK [SKIP_FRAMEWORK ...]]
               [-c CHECK] [--skip-check SKIP_CHECK]
               [--run-all-external-checks] [-s] [--soft-fail-on SOFT_FAIL_ON]
               [--hard-fail-on HARD_FAIL_ON] [--bc-api-key BC_API_KEY]
               [--prisma-api-url PRISMA_API_URL] [--skip-results-upload]
               [--docker-image DOCKER_IMAGE]
               [--dockerfile-path DOCKERFILE_PATH] [--repo-id REPO_ID]
               [-b BRANCH] [--skip-download] [--use-enforcement-rules]
               [--download-external-modules DOWNLOAD_EXTERNAL_MODULES]
               [--var-file VAR_FILE]
               [--external-modules-download-path EXTERNAL_MODULES_DOWNLOAD_PATH]
               [--evaluate-variables EVALUATE_VARIABLES] [-ca CA_CERTIFICATE]
               [--no-cert-verify]
               [--repo-root-for-plan-enrichment REPO_ROOT_FOR_PLAN_ENRICHMENT]
               [--config-file CONFIG_FILE] [--create-config CREATE_CONFIG]
               [--show-config] [--create-baseline] [--baseline BASELINE]
               [--output-baseline-as-skipped]
               [--skip-cve-package SKIP_CVE_PACKAGE]
               [--policy-metadata-filter POLICY_METADATA_FILTER]
               [--policy-metadata-filter-exception POLICY_METADATA_FILTER_EXCEPTION]
               [--secrets-scan-file-type SECRETS_SCAN_FILE_TYPE]
               [--enable-secret-scan-all-files]
               [--block-list-secret-scan BLOCK_LIST_SECRET_SCAN]
               [--summary-position {bottom,top}]
               [--skip-resources-without-violations] [--deep-analysis]
               [--no-fail-on-crash] [--mask MASK] [--scan-secrets-history]
               [--secrets-history-timeout SECRETS_HISTORY_TIMEOUT]
               [--custom-tool-name CUSTOM_TOOL_NAME]
checkov: error: argument -f/--file: expected at least one argument
❌ REPOSITORY / devskim - 2027 errors

No output available

❌ REPOSITORY / grype - 2 errors

No output available

❌ COPYPASTE / jscpd - 70 errors
ion.http/agent.injection.http_header.c [192:106 - 198:25]
Clone found (c)
 - src/usr/share/opentelemetry_shell/agent.instrumentation.http/agent.injection.http_header.c [175:77 - 181:25] (7 lines, 52 tokens)
   src/usr/share/opentelemetry_shell/agent.instrumentation.http/agent.injection.http_header.c [209:102 - 215:25]
Clone found (java)
 - src/usr/share/opentelemetry_shell/agent.instrumentation.java/GradleHttpPropagationAgent.java [13:75 - 18:7] (6 lines, 75 tokens)
   src/usr/share/opentelemetry_shell/agent.instrumentation.java/RootContextAgent.java [3:73 - 9:7]
Clone found (javascript)
 - src/usr/share/opentelemetry_shell/agent.instrumentation.node/deep.instrument.js [15:1 - 36:2] (22 lines, 141 tokens)
   src/usr/share/opentelemetry_shell/agent.instrumentation.node/deep.link.js [11:1 - 32:2]
Clone found (bash)
 - src/usr/share/opentelemetry_shell/agent.instrumentation.wget.sh [97:114 - 104:29] (8 lines, 56 tokens)
   src/usr/share/opentelemetry_shell/agent.instrumentation.wget.sh [181:72 - 188:29]
Clone found (bash)
 - src/usr/share/opentelemetry_shell/agent.instrumentation.wget.sh [118:9 - 124:90] (7 lines, 57 tokens)
   src/usr/share/opentelemetry_shell/agent.instrumentation.wget.sh [129:7 - 135:88]
Clone found (bash)
 - src/usr/share/opentelemetry_shell/agent.sh [343:19 - 356:2] (14 lines, 59 tokens)
   src/usr/share/opentelemetry_shell/agent.sh [362:27 - 375:2]
Clone found (python)
 - src/usr/share/opentelemetry_shell/sdk.py [65:9 - 87:42] (23 lines, 141 tokens)
   src/usr/share/opentelemetry_shell/sdk.py [105:9 - 128:37]
Clone found (bash)
 - tests/assert.sh [37:45 - 54:8] (18 lines, 79 tokens)
   tests/assert.sh [54:44 - 71:8]
Clone found (bash)
 - tests/auto/test_auto_curl.sh [7:45 - 17:14] (11 lines, 97 tokens)
   tests/auto/test_auto_wget.sh [9:50 - 18:14]
Clone found (bash)
 - tests/auto/test_auto_curl.sh [12:1 - 17:14] (6 lines, 62 tokens)
   tests/auto/test_auto_curl.sh [66:1 - 71:14]
Clone found (bash)
 - tests/auto/test_auto_curl.sh [17:43 - 22:89] (6 lines, 60 tokens)
   tests/auto/test_auto_curl.sh [71:41 - 76:89]
Clone found (bash)
 - tests/auto/test_auto_curl.sh [19:19 - 25:84] (7 lines, 80 tokens)
   tests/auto/test_auto_curl.sh [39:29 - 45:84]
Clone found (bash)
 - tests/auto/test_auto_curl.sh [30:61 - 35:14] (6 lines, 54 tokens)
   tests/auto/test_auto_curl.sh [64:68 - 69:14]
Clone found (bash)
 - tests/auto/test_auto_curl.sh [32:1 - 37:14] (6 lines, 62 tokens)
   tests/auto/test_auto_wget.sh [32:1 - 37:14]
Clone found (bash)
 - tests/auto/test_auto_curl.sh [49:1 - 54:14] (6 lines, 62 tokens)
   tests/auto/test_auto_wget.sh [49:1 - 54:14]
Clone found (bash)
 - tests/auto/test_auto_injection_node.sh [67:1 - 79:26] (13 lines, 65 tokens)
   tests/auto/test_auto_injection_node.sh [98:1 - 110:26]
Clone found (bash)
 - tests/auto/test_auto_injection_node.sh [80:1 - 98:6] (19 lines, 117 tokens)
   tests/auto/test_auto_injection_node.sh [112:1 - 130:6]
Clone found (bash)
 - tests/auto/test_auto_injection_node.sh [109:9 - 115:14] (7 lines, 54 tokens)
   tests/auto/test_auto_injection_node.sh [135:2 - 141:14]
Clone found (bash)
 - tests/auto/test_auto_netcat.sh [98:19 - 104:193] (7 lines, 69 tokens)
   tests/auto/test_auto_netcat.sh [109:33 - 115:193]
Clone found (bash)
 - tests/auto/test_auto_wget.sh [20:19 - 28:37] (9 lines, 92 tokens)
   tests/auto/test_auto_wget.sh [39:29 - 48:20]
┌────────────┬────────────────┬─────────────┬──────────────┬──────────────┬──────────────────┬───────────────────┐
│ Format     │ Files analyzed │ Total lines │ Total tokens │ Clones found │ Duplicated lines │ Duplicated tokens │
├────────────┼────────────────┼─────────────┼──────────────┼──────────────┼──────────────────┼───────────────────┤
│ bash       │ 108            │ 8288        │ 58528        │ 58           │ 605 (7.30%)      │ 5907 (10.09%)     │
├────────────┼────────────────┼─────────────┼──────────────┼──────────────┼──────────────────┼───────────────────┤
│ c          │ 2              │ 334         │ 2652         │ 4            │ 26 (7.78%)       │ 236 (8.90%)       │
├────────────┼────────────────┼─────────────┼──────────────┼──────────────┼──────────────────┼───────────────────┤
│ java       │ 6              │ 313         │ 2886         │ 2            │ 10 (3.19%)       │ 142 (4.92%)       │
├────────────┼────────────────┼─────────────┼──────────────┼──────────────┼──────────────────┼───────────────────┤
│ javascript │ 9              │ 296         │ 2690         │ 5            │ 69 (23.31%)      │ 632 (23.49%)      │
├────────────┼────────────────┼─────────────┼──────────────┼──────────────┼──────────────────┼───────────────────┤
│ kotlin     │ 2              │ 57          │ 703          │ 0            │ 0 (0.00%)        │ 0 (0.00%)         │
├────────────┼────────────────┼─────────────┼──────────────┼──────────────┼──────────────────┼───────────────────┤
│ python     │ 3              │ 733         │ 5265         │ 1            │ 22 (3.00%)       │ 141 (2.68%)       │
├────────────┼────────────────┼─────────────┼──────────────┼──────────────┼──────────────────┼───────────────────┤
│ txt        │ 2              │ 16          │ 134          │ 0            │ 0 (0.00%)        │ 0 (0.00%)         │
├────────────┼────────────────┼─────────────┼──────────────┼──────────────┼──────────────────┼───────────────────┤
│ Total:     │ 132            │ 10037       │ 72858        │ 70           │ 732 (7.29%)      │ 7058 (9.69%)      │
└────────────┴────────────────┴─────────────┴──────────────┴──────────────┴──────────────────┴───────────────────┘
Found 70 clones.
HTML report saved to megalinter-reports/copy-paste/jscpd-report.html
ERROR: jscpd found too many duplicates (7.3%) over threshold (0.0%)
time: 264.011ms

(Truncated to last 5714 characters out of 14586)
❌ REPOSITORY / kingfisher - 1 error

No output available

❌ REPOSITORY / osv-scanner - 4 errors
Scanning dir .
Starting filesystem walk for root: /
Scanned src/opt/opentelemetry_shell/requirements.txt file and found 8 packages
Scanned src/usr/share/opentelemetry_shell/agent.instrumentation.java/pom.xml file and found 2 packages
Scanned src/usr/share/opentelemetry_shell/agent.instrumentation.python/requirements.txt file and found 8 packages
Scanned src/usr/share/opentelemetry_shell/agent.instrumentation.python/instrumentation_roots_requirements.txt file and found 2 packages
Scanned actions/instrument/job/package-lock.json file and found 157 packages
End status: 92 dirs visited, 535 inodes visited, 5 Extract calls, 36.332284ms elapsed, 36.332534ms wall time
Warning: enricher transitivedependency/pomxml may be risky when run on untrusted artifacts. Please ensure you trust the source code and artifacts.

Total 4 packages affected by 4 known vulnerabilities (0 Critical, 2 High, 2 Medium, 0 Low, 0 Unknown) from 2 ecosystems.
4 vulnerabilities can be fixed.

+-------------------------------------+------+-----------+-----------------+---------+---------------+---------------------------------------------------------------------------------+
| OSV URL                             | CVSS | ECOSYSTEM | PACKAGE         | VERSION | FIXED VERSION | SOURCE                                                                          |
+-------------------------------------+------+-----------+-----------------+---------+---------------+---------------------------------------------------------------------------------+
| https://osv.dev/PYSEC-2026-215      | 6.9  | PyPI      | idna            | 3.9.0   | 3.15          | src/opt/opentelemetry_shell/requirements.txt                                    |
| https://osv.dev/GHSA-65pc-fj4g-8rjx |      |           |                 |         |               |                                                                                 |
| https://osv.dev/PYSEC-2026-215      | 6.9  | PyPI      | idna            | 3.9.0   | 3.15          | src/usr/share/opentelemetry_shell/agent.instrumentation.python/requirements.txt |
| https://osv.dev/GHSA-65pc-fj4g-8rjx |      |           |                 |         |               |                                                                                 |
| https://osv.dev/GHSA-mh99-v99m-4gvg | 7.5  | npm       | brace-expansion | 1.1.16  | 5.0.8         | actions/instrument/job/package-lock.json                                        |
| https://osv.dev/GHSA-mh99-v99m-4gvg | 7.5  | npm       | brace-expansion | 2.1.2   | 5.0.8         | actions/instrument/job/package-lock.json                                        |
+-------------------------------------+------+-----------+-----------------+---------+---------------+---------------------------------------------------------------------------------+
❌ REPOSITORY / trivy - 11 errors

No output available

Notices

📣 MegaLinter 9.5.0 is out! Discover the new features and security recommendations in the release announcement. (Skip this info by defining SECURITY_SUGGESTIONS: false)

See detailed reports in MegaLinter artifacts
Set VALIDATE_ALL_CODEBASE: true in mega-linter.yml to validate all sources, not only the diff

MegaLinter is graciously provided by OX Security
Show us your support by starring ⭐ the repository

- Create .mega-linter.yml with SHELL_SHFMT_ARGUMENTS="-i 2 -ci" (2-space indent,
  case-indent style matching codebase conventions)
- Add SPELL_LYCHEE_FILTER_REGEX_EXCLUDE to skip lychee URL checks in .github/workflows/
- Mark demos/injection_deep_gradle/gradlew as generated in .gitattributes
- Fix #!/bin/sh -> #!/bin/bash in decorate_action.sh (uses bash-only ${!1} and $'\n')
- Run shfmt -w -i 2 -ci on all 74 shell files to apply consistent formatting
Copilot AI changed the title [WIP] Fix shfmt formatting issues in shell files Apply shfmt formatting and configure MegaLinter shfmt style Jul 27, 2026
Copilot AI requested a review from plengauer July 27, 2026 16:10
@plengauer
plengauer marked this pull request as ready for review July 27, 2026 19:25
Copilot AI review requested due to automatic review settings July 27, 2026 19:25
@plengauer
plengauer requested a review from moflwi as a code owner July 27, 2026 19:25
@plengauer
plengauer enabled auto-merge (squash) July 27, 2026 19:26

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Pull request overview

This PR standardizes shell formatting across the repo by configuring MegaLinter’s shfmt arguments to match the project’s 2-space indentation style, and then applying shfmt formatting broadly to reduce lint noise and keep diffs consistent.

Changes:

  • Add MegaLinter configuration for shfmt (-i 2 -ci) and lychee URL-scan exclusions.
  • Reformat a large portion of shell scripts/tests with shfmt to match the established style.
  • Adjust GitHub Actions job instrumentation scripts (including a shebang change) and mark the Gradle wrapper as generated.

Reviewed changes

Copilot reviewed 45 out of 76 changed files in this pull request and generated 3 comments.

Show a summary per file
File Description
.mega-linter.yml Adds repo-wide MegaLinter config for shfmt and lychee filtering.
.gitattributes Marks demos/injection_deep_gradle/gradlew as generated for tooling.
INSTALL.sh shfmt reformat; no intended logic changes.
meta/debian/postinst shfmt reformat; no intended logic changes.
demos/injection_deep_node/demo.sh shfmt reformat.
demos/_complex_download_github_releases/demo.sh shfmt reformat (pipeline line breaks).
actions/instrument/shared/install.sh shfmt reformat.
actions/instrument/shared/id_printer.sh shfmt reformat.
actions/instrument/shared/github.sh shfmt reformat (pipeline indentation).
actions/instrument/shared/config_validation.sh shfmt reformat.
actions/instrument/repository/main.sh shfmt reformat.
actions/instrument/checksuite/main.sh shfmt reformat; some control-flow expanded to multi-line.
actions/instrument/job/inject_and_init.sh shfmt reformat; remains bash-based script.
actions/instrument/job/shutdown.sh shfmt reformat (redirection spacing).
actions/instrument/job/decorate_action.sh Changes shebang to bash and shfmt reformat.
actions/instrument/job/decorate_action_run.sh shfmt reformat; wrapper for shell steps.
actions/instrument/job/decorate_action_node.sh shfmt reformat.
actions/instrument/job/decorate_action_docker.sh shfmt reformat.
src/usr/share/opentelemetry_shell/api.sh shfmt reformat across API helpers.
src/usr/share/opentelemetry_shell/api.observe.subprocesses.sh shfmt reformat.
src/usr/share/opentelemetry_shell/api.observe.pipes.sh shfmt reformat.
src/usr/share/opentelemetry_shell/api.observe.logs.sh shfmt reformat.
src/usr/share/opentelemetry_shell/agent.sh shfmt reformat.
src/usr/share/opentelemetry_shell/agent.instrumentation.wget.sh shfmt reformat.
src/usr/share/opentelemetry_shell/agent.instrumentation.shells.sh shfmt reformat.
src/usr/share/opentelemetry_shell/agent.instrumentation.renovate.sh shfmt reformat.
src/usr/share/opentelemetry_shell/agent.instrumentation.python.sh shfmt reformat.
src/usr/share/opentelemetry_shell/agent.instrumentation.parallel.sh shfmt reformat.
src/usr/share/opentelemetry_shell/agent.instrumentation.node.sh shfmt reformat.
src/usr/share/opentelemetry_shell/agent.instrumentation.netcat.sh shfmt reformat.
src/usr/share/opentelemetry_shell/agent.instrumentation.java.sh shfmt reformat.
src/usr/share/opentelemetry_shell/agent.instrumentation.inner.sh shfmt reformat.
src/usr/share/opentelemetry_shell/agent.instrumentation.github.copilot.sh shfmt reformat.
src/usr/share/opentelemetry_shell/agent.instrumentation.github.aw.docker.sh shfmt reformat.
src/usr/share/opentelemetry_shell/agent.instrumentation.github.actions.codeql.sh shfmt reformat.
src/usr/share/opentelemetry_shell/agent.instrumentation.git.sh shfmt reformat.
src/usr/share/opentelemetry_shell/agent.instrumentation.gh.sh shfmt reformat.
src/usr/share/opentelemetry_shell/agent.instrumentation.docker.sh shfmt reformat.
src/usr/share/opentelemetry_shell/agent.instrumentation.deep.sh shfmt reformat.
src/usr/share/opentelemetry_shell/agent.instrumentation.curl.sh shfmt reformat.
src/usr/share/opentelemetry_shell/agent.instrumentation.busybox.sh shfmt reformat.
src/usr/share/opentelemetry_shell/agent.instrumentation.bash.sh shfmt reformat.
src/usr/share/opentelemetry_shell/agent.injection.netcat.handler.sh shfmt reformat.
tests/run_tests.sh shfmt reformat; multi-line subshell/grouping for readability.
tests/assert.sh shfmt reformat; expands case arms to multi-line.
tests/unit/test_unit_install_extract_release_version.sh shfmt reformat (but currently introduces a syntax error).
tests/unit/test_unit_busybox_parses_otelapi.sh shfmt reformat (redirection spacing).
tests/sdk/test_sdk_span_error.sh Removes trailing blank line.
tests/sdk/test_sdk_resource_attributes.sh shfmt reformat (test brackets spacing).
tests/sdk/test_sdk_observe.sh shfmt reformat (redirection spacing).
tests/sdk/test_sdk_observe_pipes.sh shfmt reformat (redirection spacing).
tests/performance/test_performance_script.sh shfmt reformat (redirection spacing).
tests/integration/test_integration__thoth_list_node_images.sh shfmt reformat (subshell spacing).
tests/integration/test_integration__renovate.sh shfmt reformat (redirection spacing).
tests/integration/test_integration__philbot_stop__multi_tier_injection.sh Removes trailing blank line.
tests/integration/test_integration__philbot_postinst.sh shfmt reformat; expands inline function to multi-line.
tests/integration/test_integration__docker_run__node_alpine_http.sh shfmt reformat (redirection spacing).
tests/auto/test_auto_netcat.sh shfmt reformat (redirection spacing / case arm spacing).
tests/auto/test_auto_minimal_instrumentation.sh shfmt reformat; expands inline if blocks.
tests/auto/test_auto_lifecycle.sh Removes trailing blank line.
tests/auto/test_auto_instrument.sh shfmt reformat; splits command list across lines.
tests/auto/test_auto_injection_xargs.sh shfmt reformat (redirection spacing).
tests/auto/test_auto_injection_shebang.sh shfmt reformat (redirection spacing).
tests/auto/test_auto_injection_python.sh shfmt reformat (here-doc and redirection spacing).
tests/auto/test_auto_injection_parallel.sh shfmt reformat (blank lines and block formatting).
tests/auto/test_auto_injection_node.sh shfmt reformat (redirection spacing).
tests/auto/test_auto_injection_java.sh shfmt reformat (redirection spacing).
tests/auto/test_auto_injection_find.sh shfmt reformat (blank lines).
tests/auto/test_auto_injection_docker.sh shfmt reformat (redirection spacing).
tests/auto/test_auto_http_injection_cleanup.sh shfmt reformat (redirection spacing).
tests/auto/test_auto_background_job.sh shfmt reformat (redirection spacing).
tests/auto/test_auto_alias.sh shfmt reformat; expands inline if blocks.
tests/auto/exec.sh shfmt reformat (redirection spacing).
Comments suppressed due to low confidence (1)

tests/unit/test_unit_install_extract_release_version.sh:16

  • Syntax error: missing command separator between esac and done (currently esac done)"). This will break the test script. Add a ; (or newline) before done.

Comment thread tests/unit/test_unit_install_extract_release_version.sh
Comment thread actions/instrument/job/decorate_action_run.sh
Comment thread .mega-linter.yml
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Successfully merging this pull request may close these issues.

[MegaLinter][valid] shfmt: 99 of 164 shell files don't match shfmt's formatting

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