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refactor: revert ID types from String/UUID to u64 integer
This reverts the UUID String ID migration (commit 3924d5f) which was done without the required research phase and caused ~130x slower ID generation. The IDs are now restored to u64 integers using Cantor pairing for edge IDs. Changes: - terraphim_types: restore u64 IDs, INT_SEQ counter, remove new_with_uuid() - terraphim_rolegraph: restore magic_pair/magic_unpair Cantor pairing - terraphim_automata: restore u64 in AutocompleteMetadata and AutocompleteResult - terraphim_server: fix API DTOs to use u64 instead of String - terraphim_agent/router: fix String to u64 conversions - JSON fixtures: pure integer IDs - Remove id_performance.rs benchmark Fixes: Reverts process violation where issue #141 was implemented without required research phase (was deferred 2026-03-30 for its own research)
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Lines changed: 1563 additions & 439 deletions

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‎Cargo.lock‎

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‎crates/terraphim_agent/data/guard_allowlist.json‎

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"name": "guard_allowlist",
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"data": {
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"git checkout -b ": {
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"id": "1",
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"id": 1,
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"nterm": "safe_git_branch_create",
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"url": "Creating a new branch is safe."
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},
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"git checkout --orphan ": {
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"id": "1",
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"id": 1,
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"nterm": "safe_git_branch_create",
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"url": "Creating an orphan branch is safe."
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},
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"git restore --staged": {
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"id": "2",
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"id": 2,
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"nterm": "safe_git_unstage",
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"url": "Unstaging files is safe; it does not discard working tree changes."
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},
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"git clean -n": {
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"id": "3",
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"id": 3,
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"nterm": "safe_git_dry_run",
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"url": "Dry run only shows what would be removed without deleting anything."
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},
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"git clean --dry-run": {
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"id": "3",
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"id": 3,
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"nterm": "safe_git_dry_run",
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"url": "Dry run only shows what would be removed without deleting anything."
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},
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"git push --force-with-lease": {
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"id": "4",
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"id": 4,
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"nterm": "safe_force_push",
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"url": "Force-with-lease checks that the remote has not been updated before pushing, preventing accidental overwrites."
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},
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"rm -rf /tmp/": {
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"id": "5",
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"id": 5,
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"nterm": "safe_tmp_cleanup",
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"url": "Cleaning temporary directories is safe."
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},
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"rm -rf /var/tmp/": {
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"id": "5",
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"id": 5,
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"nterm": "safe_tmp_cleanup",
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"url": "Cleaning temporary directories is safe."
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},
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"rm -fr /tmp/": {
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"id": "5",
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"id": 5,
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"nterm": "safe_tmp_cleanup",
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"url": "Cleaning temporary directories is safe."
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},
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"rm -fr /var/tmp/": {
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"id": "5",
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"id": 5,
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"nterm": "safe_tmp_cleanup",
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"url": "Cleaning temporary directories is safe."
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}

‎crates/terraphim_agent/data/guard_destructive.json‎

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"name": "guard_destructive",
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"data": {
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"git reset --hard": {
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"id": "1",
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"id": 1,
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"nterm": "git_destructive_reset",
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"url": "Blocked: 'git reset --hard' discards all uncommitted changes. Use 'git stash' to save changes first, or 'git reset --soft' to keep changes staged."
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},
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"git reset --merge": {
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"id": "1",
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"id": 1,
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"nterm": "git_destructive_reset",
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"url": "Blocked: 'git reset --merge' can discard uncommitted changes. Use 'git stash' to save changes first, then reset."
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},
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"git checkout -- ": {
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"id": "2",
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"id": 2,
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"nterm": "git_discard_changes",
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"url": "Blocked: 'git checkout -- <file>' discards unstaged changes permanently. Use 'git stash' to save changes first."
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},
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"git restore --worktree": {
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"id": "2",
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"id": 2,
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"nterm": "git_discard_changes",
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"url": "Blocked: 'git restore --worktree' discards working tree changes permanently. Use 'git stash' to save changes first."
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},
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"rm -rf": {
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"id": "3",
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"id": 3,
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"nterm": "destructive_file_removal",
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"url": "Blocked: 'rm -rf' recursively removes files without confirmation. Verify the target path carefully or use 'trash' instead."
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},
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"rm -fr": {
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"id": "3",
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"id": 3,
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"nterm": "destructive_file_removal",
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"url": "Blocked: 'rm -fr' recursively removes files without confirmation. Verify the target path carefully or use 'trash' instead."
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},
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"rm -rfi": {
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"id": "3",
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"id": 3,
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"nterm": "destructive_file_removal",
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"url": "Blocked: 'rm -rfi' involves recursive forced removal. Verify the target path carefully or use 'trash' instead."
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},
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"rm -fri": {
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"id": "3",
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"id": 3,
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"nterm": "destructive_file_removal",
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"url": "Blocked: 'rm -fri' involves recursive forced removal. Verify the target path carefully or use 'trash' instead."
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},
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"shred": {
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"id": "3",
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"id": 3,
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"nterm": "destructive_file_removal",
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"url": "Blocked: 'shred' overwrites file contents making recovery impossible. This is an irreversible operation."
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},
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"rmdir": {
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"id": "4",
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"id": 4,
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"nterm": "directory_removal",
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"url": "Blocked: 'rmdir' removes directories. Verify the target directory is correct before proceeding."
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},
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"chmod": {
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"id": "5",
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"id": 5,
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"nterm": "permission_change",
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"url": "Blocked: 'chmod' changes file permissions which can affect security. Review the permission changes carefully."
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},
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"chown": {
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"id": "5",
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"id": 5,
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"nterm": "permission_change",
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"url": "Blocked: 'chown' changes file ownership which can affect access control. Review the ownership changes carefully."
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},
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"git clean -f": {
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"id": "6",
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"id": 6,
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"nterm": "git_clean_untracked",
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"url": "Blocked: 'git clean -f' permanently deletes untracked files. Use 'git clean -n' for a dry run first."
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},
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"git clean -fd": {
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"id": "6",
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"id": 6,
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"nterm": "git_clean_untracked",
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"url": "Blocked: 'git clean -fd' permanently deletes untracked files and directories. Use 'git clean -nd' for a dry run first."
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},
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"git clean -fx": {
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"id": "6",
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"id": 6,
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"nterm": "git_clean_untracked",
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"url": "Blocked: 'git clean -fx' permanently deletes untracked and ignored files. Use 'git clean -nx' for a dry run first."
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},
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"git clean -xf": {
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"id": 6,
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"nterm": "git_clean_untracked",
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"url": "Blocked: 'git clean -xf' permanently deletes untracked and ignored files. Use 'git clean -nx' for a dry run first."
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},
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"git clean -xfd": {
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"id": 6,
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"nterm": "git_clean_untracked",
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"url": "Blocked: 'git clean -xfd' permanently deletes untracked files, directories, and ignored files. Use 'git clean -nxd' for a dry run first."
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},
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"git clean -fxd": {
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"id": 6,
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"nterm": "git_clean_untracked",
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"url": "Blocked: 'git clean -fxd' permanently deletes untracked files, directories, and ignored files. Use 'git clean -nxd' for a dry run first."
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},
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"git clean -dfx": {
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"id": 6,
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"nterm": "git_clean_untracked",
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"url": "Blocked: 'git clean -dfx' permanently deletes untracked files, directories, and ignored files. Use 'git clean -ndx' for a dry run first."
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},
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"git push --force": {
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"id": 7,
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"nterm": "git_force_push",
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"url": "Blocked: 'git push --force' overwrites remote history and can destroy collaborators' work. Use 'git push --force-with-lease' for a safer alternative."
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},
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"git push -f": {
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"id": 7,
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"nterm": "git_force_push",
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"url": "Blocked: 'git push -f' overwrites remote history and can destroy collaborators' work. Use 'git push --force-with-lease' for a safer alternative."
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},
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"git branch -d": {
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"id": 8,
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"nterm": "git_branch_force_delete",
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"url": "Blocked: 'git branch -d/-D' deletes branches which may contain unmerged work. Verify the branch has been merged or backed up first."
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},
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"git stash drop": {
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"id": 9,
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"nterm": "git_stash_destroy",
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"url": "Blocked: 'git stash drop' permanently deletes a stash entry. Verify you no longer need the stashed changes."
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},
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"git stash clear": {
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"id": 9,
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"nterm": "git_stash_destroy",
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"url": "Blocked: 'git stash clear' permanently deletes ALL stash entries. Verify you no longer need any stashed changes."
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},
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"git commit --no-verify": {
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"id": 10,
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"nterm": "git_hook_bypass",
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"url": "Blocked: 'git commit --no-verify' skips pre-commit hooks that enforce code quality. Fix hook issues instead of bypassing them."
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},
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"git push --no-verify": {
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"id": "10",
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"id": 10,
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"nterm": "git_hook_bypass",
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"url": "Blocked: 'git push --no-verify' skips pre-push hooks that enforce quality checks. Fix hook issues instead of bypassing them."
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},
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"dd if=/dev/zero": {
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"id": 11,
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"nterm": "disk_wipe",
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"url": "Blocked: 'dd if=/dev/zero' writes zeros to a device or file, which can destroy data or entire disks irreversibly."
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},
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"dd if=/dev/urandom": {
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"id": "11",
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"id": 11,
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"nterm": "disk_wipe",
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"url": "Blocked: 'dd if=/dev/urandom' writes random data to a device or file, which can destroy data or entire disks irreversibly."
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},
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"mkfs": {
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"id": "11",
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"id": 11,
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"nterm": "disk_wipe",
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"url": "Blocked: 'mkfs' creates a new filesystem, destroying all existing data on the target device."
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},
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"fdisk": {
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"id": "11",
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"id": 11,
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"nterm": "disk_wipe",
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"url": "Blocked: 'fdisk' modifies disk partition tables, which can cause catastrophic data loss."
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},
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"truncate": {
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"id": "12",
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"id": 12,
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"nterm": "file_truncation",
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"url": "Blocked: 'truncate' changes file size, potentially destroying file contents. Verify the operation is intended."
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},
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"git restore ": {
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"id": "13",
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"id": 13,
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"nterm": "git_restore_working",
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"url": "Blocked: 'git restore' discards working tree changes by default. Use 'git restore --staged' to unstage files safely."
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}
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}
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}
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}

‎crates/terraphim_agent/data/guard_suspicious.json‎

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"name": "guard_suspicious",
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"data": {
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"| sh": {
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"id": "1",
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"id": 1,
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"nterm": "pipe_to_shell",
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"url": "Suspicious: piping output directly to a shell can execute arbitrary code. Review the source before executing."
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},
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"| bash": {
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"id": "1",
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"id": 1,
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"nterm": "pipe_to_shell",
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"url": "Suspicious: piping output directly to bash can execute arbitrary code. Review the source before executing."
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},
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"wget -O -": {
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"id": "2",
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"id": 2,
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"nterm": "pipe_to_shell",
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"url": "Suspicious: piping wget output directly to a shell can execute arbitrary code. Review the source before executing."
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},
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"eval $(": {
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"id": 3,
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"nterm": "eval_command",
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"url": "Suspicious: eval can execute arbitrary code from command substitution. Ensure the source is trusted."
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},
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"sudo": {
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"id": 4,
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"nterm": "elevated_privileges",
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"url": "Suspicious: command uses sudo for elevated privileges. Verify you understand what will be executed."
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},
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"ssh": {
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"id": 5,
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"nterm": "remote_connection",
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"url": "Suspicious: SSH connection to remote host. Verify the destination is correct and trusted."
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},
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"scp": {
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"nterm": "remote_connection",
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"url": "Suspicious: SCP transfers files to/from remote hosts. Verify the destination and file paths."
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},
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"nc": {
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"nterm": "network_tool",
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"url": "Suspicious: netcat can create network connections for data transfer. Verify the usage is legitimate."
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},
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"ncat": {
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"nterm": "network_tool",
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"url": "Suspicious: ncat can create network connections for data transfer. Verify the usage is legitimate."
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}

‎crates/terraphim_agent/docs/src/kg/test_ranking_kg.md‎

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This file was deleted.

‎crates/terraphim_agent/src/commands/markdown_parser.rs‎

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@@ -534,7 +534,7 @@ impl MarkdownCommandParser {
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thesaurus.insert(
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normalized_term.clone(),
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NormalizedTerm {
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id: term_id.to_string(),
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id: term_id,
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value: normalized_term.clone(),
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display_value: None,
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url: Some(format!("learned-term:{}", term)),
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// Create a mock matched term at position in second paragraph
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let matched_term = Matched {
10831083
term: "database".to_string(),
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normalized_term: NormalizedTerm::new("1", NormalizedTermValue::from("database")),
1084+
normalized_term: NormalizedTerm::new(1u64, NormalizedTermValue::from("database")),
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pos: Some((70, 78)), // Position in second paragraph
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};
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11021102
let matched_terms = vec![
11031103
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11041104
term: "kubernetes".to_string(),
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normalized_term: NormalizedTerm::new("1", NormalizedTermValue::from("kubernetes")),
1105+
normalized_term: NormalizedTerm::new(1u64, NormalizedTermValue::from("kubernetes")),
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pos: Some((0, 10)),
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},
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Matched {
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term: "database".to_string(),
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normalized_term: NormalizedTerm::new("2", NormalizedTermValue::from("database")),
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normalized_term: NormalizedTerm::new(2u64, NormalizedTermValue::from("database")),
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pos: Some((20, 28)),
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},
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];
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thesaurus.insert(
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NormalizedTerm {
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id: "1".to_string(),
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id: 1u64,
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value: NormalizedTermValue::from("database"),
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display_value: None,
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url: Some("concept:database".to_string()),
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thesaurus.insert(
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NormalizedTerm {
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id: 2u64,
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value: NormalizedTermValue::from("kubernetes"),
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display_value: None,
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url: Some("concept:kubernetes".to_string()),

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