chore: harden agent hardlink automation #334

Coldaine · 2026-01-01T00:48:29Z

User description

Addresses bot-flagged robustness items for agent instruction mirroring + does a quick documentation consistency pass.

Changes:

Make hardlink scripts portable (non-GNU stat), louder on failures, and idempotent.
Stop suppressing hook output; use --quiet mode instead.
Improve docs-ci mirror drift errors with actionable hints.
Align docs/plans + playbook language with current policy (AGENTS.md canonical; no docs/agents.md).
Clean up README duplication and remove conflicting STT claims.
Update CI split guidance in AGENTS.md + CI architecture doc.

PR Type

Enhancement, Bug fix

Description

Harden agent hardlink automation with portable stat, fallback copy, and idempotency checks
Replace output suppression with explicit --quiet flag for better control
Improve docs-ci mirror drift errors with actionable hints and error context
Align documentation policy: AGENTS.md canonical; remove conflicting docs/agents.md references
Update CI architecture guidance: move cargo build and unit tests to GitHub-hosted runners
Simplify README: remove outdated STT claims and consolidate development setup

Diagram Walkthrough

flowchart LR
  A["Hardlink Scripts"] -->|"Add --quiet flag"| B["Quiet Mode Control"]
  A -->|"Portable stat + fallback"| C["Cross-Platform Support"]
  A -->|"Idempotency checks"| D["Robustness"]
  E["CI Validation"] -->|"Better error messages"| F["Actionable Hints"]
  G["Documentation"] -->|"AGENTS.md canonical"| H["Single Source of Truth"]
  G -->|"Remove docs/agents.md refs"| H
  I["CI Architecture"] -->|"GitHub-hosted for build/tests"| J["Optimized Parallelism"]

File Walkthrough

Relevant files

Enhancement, error handling

2 files

ensure_agent_hardlinks.sh `Harden hardlink script with portability and robustness`	+98/-6
docs-ci.yml `Add actionable error hints for mirror drift detection`	+10/-2

Enhancement

4 files

install_git_hardlink_hooks.sh `Add quiet mode and improve hook configuration output`	+16/-3
post-checkout `Use explicit quiet flag instead of output redirection`	+1/-1
post-merge `Use explicit quiet flag instead of output redirection`	+1/-1
mise.toml `Use quiet flag for hardlink hook installation`	+1/-1

Documentation

9 files

copilot-instructions.md `Update CI split guidance for build and unit tests`	+1/-1
agents.md `Update CI split guidance for build and unit tests`	+1/-1
AGENTS.md `Update CI split guidance for build and unit tests`	+1/-1
README.md `Simplify and remove outdated STT documentation claims`	+10/-97
MasterDocumentationPlaybook.md `Clarify hardlink mirrors policy and remove docs/agents.md`	+3/-3
architecture.md `Restructure CI split rationale and move build to GitHub-hosted`	+34/-39
documentation-migration-mapping.md `Add override note on canonical AGENTS.md policy`	+7/-2
future-documentation-architecture.md `Add override note removing docs/agents.md from future state`	+5/-1
proposal-documentation-restructure.md `Add override note on canonical AGENTS.md and remove docs/agents.md`	+10/-6

chatgpt-codex-connector · 2026-01-01T00:48:37Z

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qodo-free-for-open-source-projects · 2026-01-01T00:48:59Z

PR Compliance Guide 🔍

Below is a summary of compliance checks for this PR:

Security Compliance
⚪	Symlink following vulnerability Description: The `ln -f` command can follow symlinks and overwrite arbitrary files if `$dst` is a symlink pointing outside the repository, potentially allowing an attacker to overwrite system files or sensitive data by manipulating symlinks before running the script. ensure_agent_hardlinks.sh [65-73] Referred Code if ln -f "$src" "$dst" 2>/dev/null; then return 0 fi # If hardlinking fails (e.g., cross-filesystem), keep content correct but warn. cp -f "$src" "$dst" echo "warning: could not hardlink $dst; copied contents instead" >&2 return 0 }
	TOCTOU race condition Description: The script exits with error if content doesn't match after `link_or_copy`, but an attacker could exploit race conditions between the copy/link operation and the `cmp` check to inject malicious content into agent instruction files that are executed by AI agents. ensure_agent_hardlinks.sh [96-99] Referred Code if ! cmp -s "$src" "$dst"; then echo "error: $dst does not match $src" >&2 exit 1 fi
	Command injection via error output Description: Error messages containing user-controlled paths or filenames are output without sanitization, which could allow injection of GitHub Actions workflow commands through specially crafted branch names or file paths (e.g., `::set-output name=x::value`). docs-ci.yml [44-53] Referred Code if ! diff -u AGENTS.md .github/copilot-instructions.md; then echo "::error::Agent instruction mirror drift: .github/copilot-instructions.md differs from AGENTS.md" echo "hint: run ./scripts/ensure_agent_hardlinks.sh (or mise run prepare)" >&2 exit 1 fi if ! diff -u AGENTS.md .kilocode/rules/agents.md; then echo "::error::Agent instruction mirror drift: .kilocode/rules/agents.md differs from AGENTS.md" echo "hint: run ./scripts/ensure_agent_hardlinks.sh (or mise run prepare)" >&2 exit 1 fi
Ticket Compliance
⚪	🎫 No ticket provided Create ticket/issue
Codebase Duplication Compliance
⚪	Codebase context is not defined Follow the guide to enable codebase context checks.
Custom Compliance
🟢	Generic: Comprehensive Audit Trails Objective: To create a detailed and reliable record of critical system actions for security analysis and compliance. Status: Passed Learn more about managing compliance generic rules or creating your own custom rules
	Generic: Meaningful Naming and Self-Documenting Code Objective: Ensure all identifiers clearly express their purpose and intent, making code self-documenting Status: Passed Learn more about managing compliance generic rules or creating your own custom rules
	Generic: Robust Error Handling and Edge Case Management Objective: Ensure comprehensive error handling that provides meaningful context and graceful degradation Status: Passed Learn more about managing compliance generic rules or creating your own custom rules
	Generic: Secure Error Handling Objective: To prevent the leakage of sensitive system information through error messages while providing sufficient detail for internal debugging. Status: Passed Learn more about managing compliance generic rules or creating your own custom rules
	Generic: Secure Logging Practices Objective: To ensure logs are useful for debugging and auditing without exposing sensitive information like PII, PHI, or cardholder data. Status: Passed Learn more about managing compliance generic rules or creating your own custom rules
	Generic: Security-First Input Validation and Data Handling Objective: Ensure all data inputs are validated, sanitized, and handled securely to prevent vulnerabilities Status: Passed Learn more about managing compliance generic rules or creating your own custom rules

Compliance status legend

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🟡 - Partial Compliant
🔴 - Not Compliant
⚪ - Requires Further Human Verification
🏷️ - Compliance label

qodo-code-review · 2026-01-01T00:48:59Z

PR Compliance Guide 🔍

Below is a summary of compliance checks for this PR:

Security Compliance
🟢	No security concerns identified No security vulnerabilities detected by AI analysis. Human verification advised for critical code.
Ticket Compliance
⚪	🎫 No ticket provided Create ticket/issue
Codebase Duplication Compliance
⚪	Codebase context is not defined Follow the guide to enable codebase context checks.
Custom Compliance
🟢	Generic: Comprehensive Audit Trails Objective: To create a detailed and reliable record of critical system actions for security analysis and compliance. Status: Passed Learn more about managing compliance generic rules or creating your own custom rules
	Generic: Meaningful Naming and Self-Documenting Code Objective: Ensure all identifiers clearly express their purpose and intent, making code self-documenting Status: Passed Learn more about managing compliance generic rules or creating your own custom rules
	Generic: Secure Error Handling Objective: To prevent the leakage of sensitive system information through error messages while providing sufficient detail for internal debugging. Status: Passed Learn more about managing compliance generic rules or creating your own custom rules
	Generic: Secure Logging Practices Objective: To ensure logs are useful for debugging and auditing without exposing sensitive information like PII, PHI, or cardholder data. Status: Passed Learn more about managing compliance generic rules or creating your own custom rules
	Generic: Security-First Input Validation and Data Handling Objective: Ensure all data inputs are validated, sanitized, and handled securely to prevent vulnerabilities Status: Passed Learn more about managing compliance generic rules or creating your own custom rules
🔴	Generic: Robust Error Handling and Edge Case Management Objective: Ensure comprehensive error handling that provides meaningful context and graceful degradation Status: Quiet flag bug: The call `"$repo_root/scripts/ensure_agent_hardlinks.sh" ${quiet:+--quiet}` always expands `--quiet` because `quiet` is set to `0`/`1` (non-empty), preventing intended non-quiet behavior and masking expected output in error/diagnostic scenarios. Referred Code "$repo_root/scripts/ensure_agent_hardlinks.sh" ${quiet:+--quiet} Learn more about managing compliance generic rules or creating your own custom rules

Compliance status legend

🟢 - Fully Compliant
🟡 - Partial Compliant
🔴 - Not Compliant
⚪ - Requires Further Human Verification
🏷️ - Compliance label

qodo-free-for-open-source-projects · 2026-01-01T00:49:59Z

PR Code Suggestions ✨

Explore these optional code suggestions:

Category Suggestion Impact

Possible issue

Fix contradictory hardlink fallback logic

Fix the contradictory logic in ensure_agent_hardlinks.sh where the fallback to
copying a file still results in an error because a hardlink is expected.

scripts/ensure_agent_hardlinks.sh [57-106]

 link_or_copy() {
   local dst="$1"
 
   # Remove symlinks explicitly; ln -f replaces regular files but not all symlinks reliably.
   if [[ -L "$dst" ]]; then
     rm -f "$dst"
   fi
 
   if ln -f "$src" "$dst" 2>/dev/null; then
-    return 0
+    return 0 # 0 for hardlinked
   fi
 
   # If hardlinking fails (e.g., cross-filesystem), keep content correct but warn.
   cp -f "$src" "$dst"
   echo "warning: could not hardlink $dst; copied contents instead" >&2
-  return 0
+  return 1 # 1 for copied
 }
 
 is_hardlinked_pair() {
   local a="$1"
   local b="$2"
 
   local ia ib
   if ia="$(inode_of "$a")" && ib="$(inode_of "$b")"; then
     [[ "$ia" == "$ib" ]]
     return $?
   fi
 
   # Fallback: inode via ls -i (portable enough for typical *nix).
   ia="$(ls -di "$a" 2>/dev/null | awk '{print $1}')" || return 1
   ib="$(ls -di "$b" 2>/dev/null | awk '{print $1}')" || return 1
-  [[ "$ia" == "$ib" ]]
+  [[ -n "$ia" && "$ia" == "$ib" ]]
 }
 
 ensure_pair() {
   local dst="$1"
 
-  link_or_copy "$dst"
-
-  if ! cmp -s "$src" "$dst"; then
-    echo "error: $dst does not match $src" >&2
-    exit 1
+  if ! link_or_copy "$dst"; then
+    # This block runs if hardlinking failed and a copy was made.
+    # The copy is acceptable, but we should verify it.
+    if ! cmp -s "$src" "$dst"; then
+      echo "error: $dst was copied but does not match $src" >&2
+      exit 1
+    fi
+    # The copy is valid, so we don't exit with an error.
+    return 0
   fi
 
+  # This block runs if hardlinking succeeded.
   if ! is_hardlinked_pair "$src" "$dst"; then
     echo "error: $dst is not hardlinked to $src (same contents, different inode)" >&2
     echo "hint: ensure both files are on the same filesystem; rerun scripts/ensure_agent_hardlinks.sh" >&2
     exit 2
   fi
 }

Apply / Chat

Suggestion importance[1-10]: 9

__

Why: The suggestion correctly identifies a critical logic flaw in the new ensure_agent_hardlinks.sh script where the copy fallback mechanism is rendered useless by a subsequent hardlink check, causing the script to fail.

High

More

qodo-code-review · 2026-01-01T00:50:07Z

PR Code Suggestions ✨

Explore these optional code suggestions:

Category	Suggestion	Impact
Possible issue	Fix hardlink check after copy fallback Modify `link_or_copy` to return a status indicating whether it created a hardlink or fell back to a copy. Then, update `ensure_pair` to only enforce the hardlink check when a hardlink was successfully created. scripts/ensure_agent_hardlinks.sh [91-106] +link_or_copy() { + local dst="$1" + + # Remove symlinks explicitly; ln -f replaces regular files but not all symlinks reliably. + if [[ -L "$dst" ]]; then + rm -f "$dst" + fi + + if ln -f "$src" "$dst" 2>/dev/null; then + return 0 # 0 for hardlink success + fi + + # If hardlinking fails (e.g., cross-filesystem), keep content correct but warn. + cp -f "$src" "$dst" + echo "warning: could not hardlink $dst; copied contents instead" >&2 + return 1 # 1 for copy fallback +} + +# ... + ensure_pair() { local dst="$1" + local link_status=0 - link_or_copy "$dst" + link_or_copy "$dst" \|\| link_status=$? if ! cmp -s "$src" "$dst"; then echo "error: $dst does not match $src" >&2 exit 1 fi - if ! is_hardlinked_pair "$src" "$dst"; then - echo "error: $dst is not hardlinked to $src (same contents, different inode)" >&2 - echo "hint: ensure both files are on the same filesystem; rerun scripts/ensure_agent_hardlinks.sh" >&2 - exit 2 + if [[ "$link_status" -eq 0 ]]; then # Only enforce hardlink if link_or_copy succeeded in linking + if ! is_hardlinked_pair "$src" "$dst"; then + echo "error: $dst is not hardlinked to $src (same contents, different inode)" >&2 + echo "hint: ensure both files are on the same filesystem; rerun scripts/ensure_agent_hardlinks.sh" >&2 + exit 2 + fi fi } `[To ensure code accuracy, apply this suggestion manually]` Suggestion importance[1-10]: 8 __ Why: The suggestion correctly identifies a significant logic bug where the script would error out even when its copy-fallback mechanism is correctly triggered, making the script fail in valid cross-filesystem scenarios.	Medium
Possible issue	Correctly pass the quiet flag Correct the logic for passing the `--quiet` flag to the sub-script. Use an array to build arguments conditionally, ensuring the flag is only added when `$quiet` is `1`. scripts/install_git_hardlink_hooks.sh [38] -"$repo_root/scripts/ensure_agent_hardlinks.sh" ${quiet:+--quiet} +args=() +if [[ "$quiet" -eq 1 ]]; then + args+=(--quiet) +fi +"$repo_root/scripts/ensure_agent_hardlinks.sh" "${args[@]}" Apply / Chat Suggestion importance[1-10]: 7 __ Why: The suggestion correctly identifies a bug where the `--quiet` flag is always passed to a sub-script due to incorrect shell parameter expansion, and provides a correct fix.	Medium
General	Avoid redundant stat command calls Improve script performance by detecting the `stat` command variant (GNU vs. BSD) once at startup. Store the correct format flags in variables to avoid redundant `stat` calls within the `inode_of` and `link_count_of` functions. scripts/ensure_agent_hardlinks.sh [31-55] +# ... (script start) + +# Detect stat format once +if stat -c '%i' . >/dev/null 2>&1; then + STAT_INODE_FMT='%i' + STAT_LINKS_FMT='%h' +elif stat -f '%i' . >/dev/null 2>&1; then + STAT_INODE_FMT='%i' + STAT_LINKS_FMT='%l' +else + STAT_INODE_FMT='' + STAT_LINKS_FMT='' +fi + +say() { +# ... + inode_of() { local path="$1" - if stat -c '%i' "$path" >/dev/null 2>&1; then - stat -c '%i' "$path" - return 0 - fi - if stat -f '%i' "$path" >/dev/null 2>&1; then - stat -f '%i' "$path" - return 0 + if [[ -n "$STAT_INODE_FMT" ]]; then + stat -f "$STAT_INODE_FMT" "$path" 2>/dev/null \|\| stat -c "$STAT_INODE_FMT" "$path" 2>/dev/null + return $? fi return 1 } link_count_of() { local path="$1" - if stat -c '%h' "$path" >/dev/null 2>&1; then - stat -c '%h' "$path" - return 0 - fi - if stat -f '%l' "$path" >/dev/null 2>&1; then - stat -f '%l' "$path" - return 0 + if [[ -n "$STAT_LINKS_FMT" ]]; then + stat -f "$STAT_LINKS_FMT" "$path" 2>/dev/null \|\| stat -c "$STAT_LINKS_FMT" "$path" 2>/dev/null + return $? fi return 1 } +# ... (rest of script) + `[To ensure code accuracy, apply this suggestion manually]` Suggestion importance[1-10]: 4 __ Why: The suggestion offers a valid micro-optimization to reduce redundant `stat` calls, improving script efficiency and portability, but the performance impact is likely negligible for this use case.	Low
More

kiloconnect · 2026-01-01T00:50:24Z

✅ No Issues Found

15 files reviewed | Confidence: 95% | Recommendation: Approved

Review Details

Files Changed:

Scripts: ensure_agent_hardlinks.sh, install_git_hardlink_hooks.sh, .githooks/post-checkout, .githooks/post-merge, mise.toml
CI/CD: .github/workflows/docs-ci.yml
Documentation: AGENTS.md, .github/copilot-instructions.md, .kilocode/rules/agents.md, README.md, docs/MasterDocumentationPlaybook.md, docs/dev/CI/architecture.md, docs/plans/documentation-migration-mapping.md, docs/plans/future-documentation-architecture.md, docs/plans/proposal-documentation-restructure.md

Checked: Script robustness, portability, error handling, documentation consistency, CI configuration

Summary: This PR successfully hardens agent hardlink automation with significant improvements to portability, robustness, and user experience. All changes are improvements with no issues identified.

Key Improvements:

Script Hardening: Portable stat commands (GNU/BSD), fallback copying for cross-filesystem scenarios, idempotency validation
Better UX: Explicit --quiet flag replacing output redirection, actionable error messages with hints
Documentation: CI split updates, simplified README, clarified AGENTS.md canonical policy
CI: Enhanced error messages in docs validation workflow

PR Status: ✅ Already merged successfully on 2026-01-01

Copilot

Pull request overview

This PR hardens the agent instruction mirroring automation and improves documentation consistency across the repository. The changes focus on making hardlink management scripts more robust, portable, and informative while aligning documentation with the current policy that AGENTS.md is the canonical source at the repo root.

Key Changes:

Enhanced hardlink scripts with portable stat detection, better error messages, and --quiet mode support
Updated CI split guidance to reflect that builds and unit tests run on GitHub-hosted runners (only hardware tests on self-hosted)
Consolidated README to remove duplication and outdated STT claims

Reviewed changes

Copilot reviewed 15 out of 15 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
`scripts/ensure_agent_hardlinks.sh`	Major refactor: adds portable stat detection (GNU/BSD), hardlink verification, copy fallback, and actionable error messages
`scripts/install_git_hardlink_hooks.sh`	Adds --quiet mode, idempotency checks, and improved status reporting
`mise.toml`	Updates to use --quiet flag instead of output redirection
`.githooks/post-merge`	Switches from output redirection to --quiet flag
`.githooks/post-checkout`	Switches from output redirection to --quiet flag
`docs/dev/CI/architecture.md`	Updates CI split rationale: GitHub-hosted now handles builds+tests, self-hosted only for hardware tests
`AGENTS.md`	Updates CI split table to reflect new architecture
`.github/copilot-instructions.md`	Mirror of AGENTS.md CI split update
`.kilocode/rules/agents.md`	Mirror of AGENTS.md CI split update
`.github/workflows/docs-ci.yml`	Improves mirror drift error messages with actionable hints
`docs/plans/documentation/proposal-documentation-restructure.md`	Adds current-state override notes clarifying AGENTS.md policy
`docs/plans/documentation/future-documentation-architecture.md`	Adds current-state override notes clarifying AGENTS.md policy
`docs/plans/documentation-migration-mapping.md`	Adds current-state override notes clarifying AGENTS.md policy
`docs/MasterDocumentationPlaybook.md`	Clarifies that agent mirrors should be hardlinked (preferred) rather than symlinked
`README.md`	Major simplification: removes 100+ lines of duplicated/outdated content, consolidates to minimal entrypoint

Copilot · 2026-01-01T00:51:36Z

scripts/ensure_agent_hardlinks.sh

+    echo "error: $dst is not hardlinked to $src (same contents, different inode)" >&2
+    echo "hint: ensure both files are on the same filesystem; rerun scripts/ensure_agent_hardlinks.sh" >&2
+    exit 2


The script exits with status 2 if hardlinking succeeds but verification fails. However, if hardlinking initially fails in link_or_copy and falls back to copying (line 70), the subsequent verification at line 101 will always fail because the files won't be hardlinked. This creates an inconsistent behavior where the script warns about copying but then exits with an error.

Consider either:

Tracking whether a copy fallback occurred and skipping the hardlink verification for those cases

Making the hardlink verification a warning instead of an error when content matches

Exiting early after copy fallback with appropriate status

Suggested change

echo "error: $dst is not hardlinked to $src (same contents, different inode)" >&2

echo "hint: ensure both files are on the same filesystem; rerun scripts/ensure_agent_hardlinks.sh" >&2

exit 2

echo "warning: $dst is not hardlinked to $src (same contents, different inode)" >&2

echo "hint: ensure both files are on the same filesystem; rerun scripts/ensure_agent_hardlinks.sh if you require hardlinks" >&2

Copilot · 2026-01-01T00:51:37Z

scripts/install_git_hardlink_hooks.sh


-echo "Enabled repo hooks via core.hooksPath=.githooks"
-"$repo_root/scripts/ensure_agent_hardlinks.sh"
+"$repo_root/scripts/ensure_agent_hardlinks.sh" ${quiet:+--quiet}


The parameter expansion ${quiet:+--quiet} is used without quotes. While this works when the variable expands to nothing or a single word, it's safer to quote it. If the expansion ever included spaces or special characters, this could cause unexpected word splitting.

Use "${quiet:+--quiet}" instead for proper quoting.

chore: harden agent hardlink automation

e423840

Copilot AI review requested due to automatic review settings January 1, 2026 00:48

Coldaine merged commit 8bf6b9d into main Jan 1, 2026
5 of 6 checks passed

Coldaine deleted the chore/bot-fixes-doc-pass branch January 1, 2026 00:48

Copilot started reviewing on behalf of Coldaine January 1, 2026 00:48 View session

qodo-free-for-open-source-projects bot added the Review effort 3/5 label Jan 1, 2026

qodo-code-review bot added the Review effort 2/5 label Jan 1, 2026

Copilot AI reviewed Jan 1, 2026

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